GBrowse: rnorvegicus.conf

File rnorvegicus.conf, 40.2 KB (added by jvelde, 14 years ago)
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1[GENERAL]
2description   = Rattus norvegicus
3database      = scaffolds
4
5initial landmark = chr19:143000..180000
6
7default tracks = Genes
8
9# examples to show in the introduction
10examples = chr1
11           chr1:80,000..120,000
12
13# "automatic" classes to try when an unqualified identifier is given
14automatic classes = Symbol Gene Clone ID
15
16
17# try to configure the rubberband menu to query for eQTLs
18
19[DETAIL SELECT MENU]
20width = 250
21html  = <table style="width:100%">
22         <tr>
23           <th style="background:lightgrey;cell-padding:5">
24             SELECTION
25             <span style="right:0px;position:absolute;color:blue;cursor:pointer"
26                   onclick="SelectArea.prototype.cancelRubber()">
27               [X]
28             </span>
29           </th>
30         </tr>
31         <tr>
32           <td>
33             <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()">
34              Zoom in
35             </span>
36           </td>
37         </tr>
38         <tr>
39           <td>
40             <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndRecenter()">
41               Recenter on this region
42             </span>
43           </td>
44         </tr>
45         <tr>
46           <td onmouseup="SelectArea.prototype.cancelRubber()">
47             <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION" target="_BLANK">
48              Dump selection as FASTA
49             </a>
50           </td>
51         </tr>
52         <tr>
53           <td onmouseup="SelectArea.prototype.cancelRubber()">
54             <a href="/cgi-bin/eqtls/eqtls.py?action=list&what=markers&p=0.05&name=SELECTION" target="_BLANK">
55              eQTL markers in selection
56             </a>
57           </td>
58         </tr>
59         <tr>
60           <td onmouseup="SelectArea.prototype.cancelRubber()">
61             <a href="/cgi-bin/eqtls/eqtls.py?action=list&what=transcripts&p=0.05&name=SELECTION" target="_BLANK">
62              eQTL transcripts in selection
63             </a>
64           </td>
65         </tr>
66         <tr>
67           <td onmouseup="SelectArea.prototype.cancelRubber()">
68             <a href="/cgi-bin/eqtls.py?find=cis" target="_BLANK">
69              cis eQTLs in selection
70             </a>
71           </td>
72         </tr>
73         <tr>
74           <td onmouseup="SelectArea.prototype.cancelRubber()">
75             <a href="/cgi-bin/coding-snps/codingsnps.pl?name=SELECTION" target="_BLANK">
76              coding SNPs in selection
77             </a>
78           </td>
79         </tr>
80         <tr>
81           <td onmouseup="SelectArea.prototype.cancelRubber()">
82             <a href="http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=SELECTION" target="_BLANK">
83              molgenis region query
84             </a>
85           </td>
86         </tr>
87       </table>
88
89###
90### The last entry in the menu list is a molgenis example which creates urls:
91### .../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999
92
93#################################
94# database definitions
95#################################
96
97[scaffolds:database]
98db_adaptor    = Bio::DB::SeqFeature::Store
99db_args       = -adaptor DBI::mysql
100                -dsn     dbi:mysql:database=rn4
101                -user    apache
102
103[variations:database]
104db_adaptor    = Bio::DB::SeqFeature::Store
105db_args       = -adaptor DBI::mysql
106                -dsn     dbi:mysql:database=rn4_variations
107                -user    apache
108
109# for the SNP density plots
110aggregators = snp_density{bin:SNP:SHR}
111
112
113###############################################################################
114###   Rbm 20 databasese
115
116
117[rbm20_cluster:database]
118db_adaptor    = Bio::DB::SeqFeature::Store
119db_args       = -adaptor DBI::mysql
120                -dsn     dbi:mysql:database=rn4_rbm20_cluster
121                -user    apache
122
123
124# [rbm20:database]
125# db_adaptor    = Bio::DB::SeqFeature::Store
126# db_args       = -adaptor DBI::mysql
127#                 -dsn     dbi:mysql:database=rn4_rbm20
128#                 -user    apache
129
130#[rbm20-mutant:database]
131#db_adaptor     = Bio::DB::Sam
132#db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
133#                 -bam   /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam
134#search options = default
135#
136[rbm20-wildtype:database]
137db_adaptor     = Bio::DB::Sam
138db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
139                 -bam   /var/www/html/gbrowse2/databases/rn4/rbm20/wildtype.bam
140search options = default
141
142#[rbm20-mutant-fwd:database]
143#db_adaptor     = Bio::DB::Sam
144#db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
145#                 -bam   /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam
146#search options = default
147#
148#[rbm20-wildtype-fwd:database]
149#db_adaptor     = Bio::DB::Sam
150#db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
151#                 -bam   /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam
152#search options = default
153#
154#[rbm20-mutant-rev:database]
155#db_adaptor     = Bio::DB::Sam
156#db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
157#                 -bam   /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam
158#search options = default
159#
160#[rbm20-wildtype-rev:database]
161#db_adaptor     = Bio::DB::Sam
162#db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
163#                 -bam   /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam
164#search options = default
165
166
167
168###############################################################################
169###   histone modification databases
170
171[histones:database]
172db_adaptor    = Bio::DB::SeqFeature::Store
173db_args       = -adaptor DBI::mysql
174                -dsn     dbi:mysql:database=rn4_histones
175                -user    apache
176
177[histones_h3k27me3:database]
178db_adaptor    = Bio::DB::SeqFeature::Store
179db_args       = -adaptor DBI::mysql
180                -dsn     dbi:mysql:database=rn4_histones_h3k27me3
181                -user    apache
182
183
184#
185[lv-H3K4me3-BN-male-bio2-tech1:database]
186db_adaptor     = Bio::DB::Sam
187db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
188                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-male-bio2-tech1-rmdup.bam
189
190[lv-H3K4me3-SHR-male-bio2-tech1:database]
191db_adaptor     = Bio::DB::Sam
192db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
193                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-male-bio2-tech1-rmdup.bam
194
195[lv-H3K4me3-BN-female-bio1-tech1:database]
196db_adaptor     = Bio::DB::Sam
197db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
198                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-female-bio1-tech1-rmdup.bam
199
200[lv-H3K4me3-SHR-female-bio1-tech1:database]
201db_adaptor     = Bio::DB::Sam
202db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
203                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-female-bio1-tech1-rmdup.bam
204
205[lv-H3K27me3-BN-male-bio2-merged:database]
206db_adaptor     = Bio::DB::Sam
207db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
208                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio2-merged.bam
209
210[lv-H3K27me3-BN-male-bio3-merged:database]
211db_adaptor     = Bio::DB::Sam
212db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
213                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio3-merged.bam
214
215[lv-H3K27me3-BN-male-bio4-merged:database]
216db_adaptor     = Bio::DB::Sam
217db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
218                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio4-merged.bam
219
220
221
222[BN-H3K4me3:database]
223db_adaptor     = Bio::DB::Sam
224db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
225                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K4me3-sorted.bam
226search options = default
227
228[BN-H3K27me3:database]
229db_adaptor     = Bio::DB::Sam
230db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
231                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K27me3-sorted.bam
232search options = default
233
234[BN-input:database]
235db_adaptor     = Bio::DB::Sam
236db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
237                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-input-sorted.bam
238search options = default
239
240[SHR-H3K4me3:database]
241db_adaptor     = Bio::DB::Sam
242db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
243                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K4me3-sorted.bam
244search options = default
245
246[SHR-H3K27me3:database]
247db_adaptor     = Bio::DB::Sam
248db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
249                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K27me3-sorted.bam
250search options = default
251
252[SHR-input:database]
253db_adaptor     = Bio::DB::Sam
254db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
255                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-input-sorted.bam
256search options = default
257
258
259[BXH12-H3K4:database]
260db_adaptor     = Bio::DB::Sam
261db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
262                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH12_sorted.bam
263search options = default
264
265[BXH02-H3K4:database]
266db_adaptor     = Bio::DB::Sam
267db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
268                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH02_sorted.bam
269search options = default
270
271[BXH03-H3K4:database]
272db_adaptor     = Bio::DB::Sam
273db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
274                 -bam   /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH03.bam
275search options = default
276
277###############################################################################
278###   micro rna databases
279
280[BN-mirna:database]
281db_adaptor     = Bio::DB::Sam
282db_args        = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
283                 -bam   /var/www/html/gbrowse2/databases/rn4/mirna/BN.csfasta__sorted.bam
284search options = default
285
286#[HXB01-mirna:database]
287#db_adaptor = Bio::DB::Sam
288#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
289#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB01.csfasta__sorted.bam
290#search options = default
291
292#[HXB03-mirna:database]
293#db_adaptor = Bio::DB::Sam
294#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
295#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB03.csfasta__sorted.bam
296#search options = default
297
298#[HXB05-mirna:database]
299#db_adaptor = Bio::DB::Sam
300#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
301#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB05.csfasta__sorted.bam
302#search options = default
303
304#[HXB10-mirna:database]
305#db_adaptor = Bio::DB::Sam
306#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
307#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB10.csfasta__sorted.bam
308#search options = default
309
310#[HXB15-mirna:database]
311#db_adaptor = Bio::DB::Sam
312#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
313#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB15.csfasta__sorted.bam
314#search options = default
315
316#[HXB18-mirna:database]
317#db_adaptor = Bio::DB::Sam
318#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
319#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB18.csfasta__sorted.bam
320#search options = default
321
322#[HXB21-mirna:database]
323#db_adaptor = Bio::DB::Sam
324#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
325#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB21.csfasta__sorted.bam
326#search options = default
327
328#[HXB23-mirna:database]
329#db_adaptor = Bio::DB::Sam
330#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
331#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB23.csfasta__sorted.bam
332#search options = default
333
334#[HXB25-mirna:database]
335#db_adaptor = Bio::DB::Sam
336#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
337#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB25.csfasta__sorted.bam
338#search options = default
339
340#[HXB29-mirna:database]
341#db_adaptor = Bio::DB::Sam
342#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
343#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB29.csfasta__sorted.bam
344#search options = default
345
346#[SHR-mirna:database]
347#db_adaptor = Bio::DB::Sam
348#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
349#-bam /var/www/html/gbrowse2/databases/rn4/mirna/SHR.csfasta__sorted.bam
350#search options = default
351
352
353
354###############################################################################
355###   track configurations
356
357# Default glyph settings
358[TRACK DEFAULTS]
359glyph       = generic
360database    = scaffolds
361height      = 8
362bgcolor     = cyan
363fgcolor     = black
364label density = 25
365bump density  = 100
366
367### TRACK CONFIGURATION ####
368# the remainder of the sections configure individual tracks
369
370
371# view the reads
372
373###############################################################################
374###   histone modifications track configurations
375
376
377# for the sex specific analysis
378[Coverage-lv-H3K4me3-BN-female-bio1-tech1]
379feature        = coverage
380glyph          = wiggle_xyplot
381database       = lv-H3K4me3-BN-female-bio1-tech1
382height         = 50
383fgcolor        = black
384bgcolor        = indigo
385key            = Coverage lv-H3K4me3-BN-female-bio1-tech1
386category       = Histone modifications
387label          = 0 # Labels on wiggle tracks are redundant.
388
389[Coverage-lv-H3K4me3-SHR-female-bio1-tech1]
390feature        = coverage
391glyph          = wiggle_xyplot
392database       = lv-H3K4me3-SHR-female-bio1-tech1
393height         = 50
394fgcolor        = black
395bgcolor        = indigo
396key            = Coverage lv-H3K4me3-SHR-female-bio1-tech1
397category       = Histone modifications
398label          = 0 # Labels on wiggle tracks are redundant.
399
400[lv-H3K4me3-BN-male-bio2-tech1]
401feature        = coverage
402glyph          = wiggle_xyplot
403database       = lv-H3K4me3-BN-male-bio2-tech1
404height         = 50
405fgcolor        = black
406bgcolor        = indigo
407key            = Coverage lv-H3K4me3-BN-male-bio2-tech1
408category       = Histone modifications
409label          = 0 # Labels on wiggle tracks are redundant.
410
411[lv-H3K4me3-SHR-male-bio2-tech1-rmdup]
412feature        = coverage
413glyph          = wiggle_xyplot
414database       = lv-H3K4me3-SHR-male-bio2-tech1
415height         = 50
416fgcolor        = black
417bgcolor        = indigo
418key            = Coverage lv-H3K4me3-SHR-male-bio2-tech1
419category       = Histone modifications
420label          = 0 # Labels on wiggle tracks are redundant.
421
422
423
424
425
426# BN
427[Coverage-lv-H3K27me3-BN-male-bio2-merged]
428feature        = coverage
429glyph          = wiggle_xyplot
430database       = lv-H3K27me3-BN-male-bio2-merged
431height         = 50
432fgcolor        = black
433bgcolor        = indigo
434key            = Coverage lv-H3K27me3-BN-male-bio2-merged
435category       = Histone modifications
436label          = 0 # Labels on wiggle tracks are redundant.
437
438[Coverage-lv-H3K27me3-BN-male-bio3-merged]
439feature        = coverage
440glyph          = wiggle_xyplot
441database       = lv-H3K27me3-BN-male-bio3-merged
442height         = 50
443fgcolor        = black
444bgcolor        = indigo
445key            = Coverage lv-H3K27me3-BN-male-bio3-merged
446category       = Histone modifications
447label          = 0 # Labels on wiggle tracks are redundant.
448
449[Coverage-lv-H3K27me3-BN-male-bio4-merged]
450feature        = coverage
451glyph          = wiggle_xyplot
452database       = lv-H3K27me3-BN-male-bio4-merged
453height         = 50
454fgcolor        = black
455bgcolor        = indigo
456key            = Coverage lv-H3K27me3-BN-male-bio4-merged
457category       = Histone modifications
458label          = 0 # Labels on wiggle tracks are redundant.
459
460
461[Coverage-BN-H3K4me3]
462feature        = coverage
463glyph          = wiggle_xyplot
464database       = BN-H3K4me3
465height         = 50
466fgcolor        = black
467bgcolor        = indigo
468key            = Coverage BN-H3K4me3
469category       = Histone modifications
470label          = 0 # Labels on wiggle tracks are redundant.
471
472# [Coverage-BN-H3K27me3]
473# feature        = coverage
474# glyph          = wiggle_xyplot
475# database       = BN-H3K27me3
476# height         = 50
477# fgcolor        = black
478# bgcolor        = indigo
479# key            = Coverage BN-H3K27me3
480# category       = Histone modifications
481# label          = 0 # Labels on wiggle tracks are redundant.
482
483[Coverage-BN-input]
484feature        = coverage
485glyph          = wiggle_xyplot
486database       = BN-input
487height         = 50
488fgcolor        = black
489bgcolor        = indigo
490key            = Coverage BN-input
491category       = Histone modifications
492label          = 0 # Labels on wiggle tracks are redundant.
493
494# [Reads-BN-H3K4me3]
495# feature        = match
496# glyph          = segments
497# draw_target    = 1
498# show_mismatch  = 1
499# mismatch_color = red
500# database       = BN-H3K4me3
501# bgcolor        = blue
502# fgcolor        = blue
503# height         = 5
504# label density  = 50
505# bump           = fast
506# key            = Reads BN-H3K4me3
507# category       = Histone modifications
508#
509# [Reads-BN-H3K27me3]
510# feature        = match
511# glyph          = segments
512# draw_target    = 1
513# show_mismatch  = 1
514# mismatch_color = red
515# database       = BN-H3K27me3
516# bgcolor        = blue
517# fgcolor        = blue
518# height         = 5
519# label density  = 50
520# bump           = fast
521# key            = Reads BN-H3K27me3
522# category       = Histone modifications
523#
524# [Reads-BN-input]
525# feature        = match
526# glyph          = segments
527# draw_target    = 1
528# show_mismatch  = 1
529# mismatch_color = red
530# database       = BN-input
531# bgcolor        = blue
532# fgcolor        = blue
533# height         = 5
534# label density  = 50
535# bump           = fast
536# key            = Reads BN-input
537# category       = Histone modifications
538
539
540# SHR reads
541
542[Coverage-SHR-H3K4me3]
543feature        = coverage
544glyph          = wiggle_xyplot
545database       = SHR-H3K4me3
546height         = 50
547fgcolor        = black
548bgcolor        = indigo
549key            = Coverage SHR-H3K4me3
550category       = Histone modifications
551label          = 0 # Labels on wiggle tracks are redundant.
552
553
554[Coverage-SHR-input]
555feature        = coverage
556glyph          = wiggle_xyplot
557database       = SHR-input
558height         = 50
559fgcolor        = black
560bgcolor        = indigo
561key            = Coverage SHR-input
562category       = Histone modifications
563label          = 0 # Labels on wiggle tracks are redundant.
564
565# [Reads-SHR-H3K4me3]
566# feature        = match
567# glyph          = segments
568# draw_target    = 1
569# show_mismatch  = 1
570# mismatch_color = red
571# database       = SHR-H3K4me3
572# bgcolor        = blue
573# fgcolor        = blue
574# height         = 5
575# label density  = 50
576# bump           = fast
577# key            = Reads SHR-H3K4me3
578# category       = Histone modifications
579#
580# [Reads-SHR-H3K27me3]
581# feature        = match
582# glyph          = segments
583# draw_target    = 1
584# show_mismatch  = 1
585# mismatch_color = red
586# database       = SHR-H3K27me3
587# bgcolor        = blue
588# fgcolor        = blue
589# height         = 5
590# label density  = 50
591# bump           = fast
592# key            = Reads SHR-H3K27me3
593# category       = Histone modifications
594#
595# [Reads-SHR-input]
596# feature        = match
597# glyph          = segments
598# draw_target    = 1
599# show_mismatch  = 1
600# mismatch_color = red
601# database       = SHR-input
602# bgcolor        = blue
603# fgcolor        = blue
604# height         = 5
605# label density  = 50
606# bump           = fast
607# key            = Reads SHR-input
608# category       = Histone modifications
609#
610#
611# # reads for the RI strains
612# [Coverage-BXH12-H3K4me3]
613# feature        = coverage
614# glyph          = wiggle_xyplot
615# database       = BXH12-H3K4
616# height         = 50
617# fgcolor        = black
618# bgcolor        = indigo
619# key            = Coverage BXH12-H3K4
620# category       = Histone modifications
621# label          = 0 # Labels on wiggle tracks are redundant.
622#
623# [Reads-BXH12-H3K4me3]
624# feature        = match
625# glyph          = segments
626# draw_target    = 1
627# show_mismatch  = 1
628# mismatch_color = red
629# database       = BXH12-H3K4
630# bgcolor        = blue
631# fgcolor        = blue
632# height         = 5
633# label density  = 50
634# bump           = fast
635# key            = Reads BXH12-H3K4me3
636# category       = Histone modifications
637#
638#
639# [Coverage-BXH02-H3K4me3]
640# feature        = coverage
641# glyph          = wiggle_xyplot
642# database       = BXH02-H3K4
643# height         = 50
644# fgcolor        = black
645# bgcolor        = indigo
646# key            = Coverage BXH102-H3K4
647# category       = Histone modifications
648# label          = 0 # Labels on wiggle tracks are redundant.
649#
650# [Reads-BXH02-H3K4me3]
651# feature        = match
652# glyph          = segments
653# draw_target    = 1
654# show_mismatch  = 1
655# mismatch_color = red
656# database       = BXH02-H3K4
657# bgcolor        = blue
658# fgcolor        = blue
659# height         = 5
660# label density  = 50
661# bump           = fast
662# key            = Reads BXH02-H3K4me3
663# category       = Histone modifications
664#
665# [Coverage-BXH03-H3K4me3]
666# feature        = coverage
667# glyph          = wiggle_xyplot
668# database       = BXH03-H3K4
669# height         = 50
670# fgcolor        = black
671# bgcolor        = indigo
672# key            = Coverage BXH103-H3K4
673# category       = Histone modifications
674# label          = 0 # Labels on wiggle tracks are redundant.
675#
676#
677# [Reads-BXH03-H3K4me3]
678# feature        = match
679# glyph          = segments
680# draw_target    = 1
681# show_mismatch  = 1
682# mismatch_color = red
683# database       = BXH03-H3K4
684# bgcolor        = blue
685# fgcolor        = blue
686# height         = 5
687# label density  = 50
688# bump           = fast
689# key            = Reads BXH03-H3K4me3
690# category       = Histone modifications
691#
692#
693# # view the results of the island calling and differential analysis
694# [sicer-BN-H3K4me3]
695# feature      = experimental_feature:sicer-BN-H3K4me3
696# database     = histones
697# glyph        = generic
698# bgcolor      = red
699# forwardcolor = red
700# reversecolor = red
701# key          = Sicer BN-H3K4me3
702# category     = Histone modifications
703#
704# [sicer-BN-H3K27me3]
705# feature      = experimental_feature:sicer-BN-H3K27me3
706# database     = histones
707# glyph        = generic
708# bgcolor      = red
709# forwardcolor = red
710# reversecolor = red
711# key          = Sicer BN-H3K27me3
712# category     = Histone modifications
713#
714# [sicer-BN-input]
715# feature      = experimental_feature:sicer-BN-input
716# database     = histones
717# glyph        = generic
718# bgcolor      = red
719# forwardcolor = red
720# reversecolor = red
721# key          = Sicer BN-input
722# category     = Histone modifications
723#
724# [sicer-SHR-H3K4me3]
725# feature      = experimental_feature:sicer-SHR-H3K4me3
726# database     = histones
727# glyph        = generic
728# bgcolor      = red
729# forwardcolor = red
730# reversecolor = red
731# key          = Sicer SHR-H3K4me3
732# category     = Histone modifications
733#
734# [sicer-SHR-H3K27me3]
735# feature      = experimental_feature:sicer-SHR-H3K27me3
736# database     = histones
737# glyph        = generic
738# bgcolor      = red
739# forwardcolor = red
740# reversecolor = red
741# key          = Sicer SHR-H3K27me3
742# category     = Histone modifications
743#
744# [sicer-SHR-input]
745# feature      = experimental_feature:sicer-SHR-input
746# database     = histones
747# glyph        = generic
748# bgcolor      = red
749# forwardcolor = red
750# reversecolor = red
751# key          = Sicer SHR-input
752# category     = Histone modifications
753#
754# [chipdiff-H3K4me3]
755# feature      = experimental_feature:chipdiff-H3K4me3
756# database     = histones
757# glyph        = generic
758# bgcolor      = red
759# forwardcolor = red
760# reversecolor = red
761# key          = Chipdiff H3K4me3
762# category     = Histone modifications
763#
764# [chipdiff-H3K27me3]
765# feature      = experimental_feature:chipdiff-H3K27me3
766# database     = histones
767# glyph        = generic
768# bgcolor      = red
769# forwardcolor = red
770# reversecolor = red
771# key          = Chipdiff H3K27me3
772# category     = Histone modifications
773#
774#
775# # tracks for the peak calls in the RI strains
776# [sicer-H3K4-BXH02]
777# feature      = experimental_feature:sicer-K4-BXH02
778# database     = histones
779# glyph        = generic
780# bgcolor      = red
781# forwardcolor = red
782# reversecolor = red
783# key          = Sicer H3K4 BXH02
784# category     = Histone modifications
785#
786#
787# [sicer-H3K4-BXH12]
788# feature      = experimental_feature:sicer-K4-BXH12
789# database     = histones
790# glyph        = generic
791# bgcolor      = red
792# forwardcolor = red
793# reversecolor = red
794# key          = Sicer H3K4 BXH12
795# category     = Histone modifications
796#
797
798
799###############################################################################
800### Binned H3K27me3 data
801
802# [binned-lv-H3K27me3-BN-male-bio4-merged-offset-3750]
803# feature        = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750
804# database       = histones_h3k27me3
805# glyph          = wiggle_xyplot
806# smoothing      = none
807# autoscale      = local       
808# bgcolor              = indigo
809# height               = 50
810# graph_type     = boxes
811# scale          = right
812# description    = 1
813# category       = Binned H3k27me3 data
814# key            = lv-H3K27me3-BN-male-bio4-merged-offset-3750
815#
816# [posterior-lv-H3K27me3-BN-male-bio4-merged-offset-3750]
817# feature        = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm
818# database       = histones_h3k27me3
819# glyph          = wiggle_xyplot
820# smoothing      = none
821# autoscale      = global
822# bicolor_pivot  = 0.99
823# pos_color      = red
824# neg_color      = gray
825# height         = 25
826# graph_type     = boxes
827# scale          = right
828# description    = 1
829# category       = Binned H3k27me3 data
830# key            = lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm
831
832#[binned-binsize-5000-posterior-lv-H3K27me3-BN-male-bio2-merged-avg-posterior]
833#feature        = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-avg-posterior-binsize-5000
834#database       = histones_h3k27me3
835#glyph          = wiggle_xyplot
836#smoothing      = none
837#autoscale      = global
838#bicolor_pivot  = 0.99
839#pos_color      = red
840#neg_color      = gray
841#height         = 25
842#graph_type     = boxes
843#scale          = right
844#description    = 1
845#category       = Binned H3k27me3 data
846#key            = lv-H3K27me3-BN-male-bio2-merged-hmm-avg-binsize-5000
847#
848#
849[binned-binsize-3000-posterior-lv-H3K27me3-BN-male-bio2-merged-offset-0-posterior]
850feature        = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000
851database       = histones_h3k27me3
852glyph          = wiggle_xyplot
853smoothing      = none
854autoscale      = global
855bicolor_pivot  = 0.99
856pos_color      = red
857neg_color      = gray
858height         = 25
859graph_type     = boxes
860scale          = right
861description    = 1
862category       = Binned H3k27me3 data
863key            = lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000
864
865
866#include "/project/intranet/gbrowse2/databases/rn4/histone-modifications/binned-data/binned-data.conf"
867
868
869###############################################################################
870###   microrna track configurations
871
872[Coverage-BN-mirna]
873feature        = coverage
874glyph          = wiggle_xyplot
875database       = BN-mirna
876height         = 50
877fgcolor        = black
878bgcolor        = indigo
879key            = Coverage BN mirna
880category       = microRNA
881label          = 0 # Labels on wiggle tracks are redundant.
882
883[Reads-BN-mirna]
884feature        = match
885glyph          = segments
886draw_target    = 1
887show_mismatch  = 1
888mismatch_color = red
889database       = BN-mirna
890bgcolor        = blue
891fgcolor        = blue
892height         = 5
893label density  = 50
894bump           = fast
895key            = Reads BN mirna
896category       = microRNA
897
898#[Coverage-HXB01-mirna]
899#feature = coverage
900#glyph = wiggle_xyplot
901#database = HXB01-mirna
902#height = 50
903#fgcolor = black
904#bgcolor = indigo
905#key = Coverage HXB01 mirna
906#category = microRNA
907#label = 0
908#
909#[Reads-HXB01-mirna]
910#feature = match
911#glyph = segments
912#draw_target = 1
913#show_mismatch = 1
914#mismatch_color = red
915#database = HXB01-mirna
916#bgcolor = blue
917#fgcolor = blue
918#height = 5
919#label density = 50
920#bump = fast
921#key = Reads HXB01 mirna
922#category = microRNA
923#
924#[Coverage-HXB03-mirna]
925#feature = coverage
926#glyph = wiggle_xyplot
927#database = HXB03-mirna
928#height = 50
929#fgcolor = black
930#bgcolor = indigo
931#key = Coverage HXB03 mirna
932#category = microRNA
933#label = 0
934#
935#[Reads-HXB03-mirna]
936#feature = match
937#glyph = segments
938#draw_target = 1
939#show_mismatch = 1
940#mismatch_color = red
941#database = HXB03-mirna
942#bgcolor = blue
943#fgcolor = blue
944#height = 5
945#label density = 50
946#bump = fast
947#key = Reads HXB03 mirna
948#category = microRNA
949#
950#[Coverage-HXB05-mirna]
951#feature = coverage
952#glyph = wiggle_xyplot
953#database = HXB05-mirna
954#height = 50
955#fgcolor = black
956#bgcolor = indigo
957#key = Coverage HXB05 mirna
958#category = microRNA
959#label = 0
960#
961#[Reads-HXB05-mirna]
962#feature = match
963#glyph = segments
964#draw_target = 1
965#show_mismatch = 1
966#mismatch_color = red
967#database = HXB05-mirna
968#bgcolor = blue
969#fgcolor = blue
970#height = 5
971#label density = 50
972#bump = fast
973#key = Reads HXB05 mirna
974#category = microRNA
975#
976#[Coverage-HXB10-mirna]
977#feature = coverage
978#glyph = wiggle_xyplot
979#database = HXB10-mirna
980#height = 50
981#fgcolor = black
982#bgcolor = indigo
983#key = Coverage HXB10 mirna
984#category = microRNA
985#label = 0
986#
987#[Reads-HXB10-mirna]
988#feature = match
989#glyph = segments
990#draw_target = 1
991#show_mismatch = 1
992#mismatch_color = red
993#database = HXB10-mirna
994#bgcolor = blue
995#fgcolor = blue
996#height = 5
997#label density = 50
998#bump = fast
999#key = Reads HXB10 mirna
1000#category = microRNA
1001#
1002#[Coverage-HXB15-mirna]
1003#feature = coverage
1004#glyph = wiggle_xyplot
1005#database = HXB15-mirna
1006#height = 50
1007#fgcolor = black
1008#bgcolor = indigo
1009#key = Coverage HXB15 mirna
1010#category = microRNA
1011#label = 0
1012#
1013#[Reads-HXB15-mirna]
1014#feature = match
1015#glyph = segments
1016#draw_target = 1
1017#show_mismatch = 1
1018#mismatch_color = red
1019#database = HXB15-mirna
1020#bgcolor = blue
1021#fgcolor = blue
1022#height = 5
1023#label density = 50
1024#bump = fast
1025#key = Reads HXB15 mirna
1026#category = microRNA
1027#
1028#[Coverage-HXB18-mirna]
1029#feature = coverage
1030#glyph = wiggle_xyplot
1031#database = HXB18-mirna
1032#height = 50
1033#fgcolor = black
1034#bgcolor = indigo
1035#key = Coverage HXB18 mirna
1036#category = microRNA
1037#label = 0
1038#
1039#[Reads-HXB18-mirna]
1040#feature = match
1041#glyph = segments
1042#draw_target = 1
1043#show_mismatch = 1
1044#mismatch_color = red
1045#database = HXB18-mirna
1046#bgcolor = blue
1047#fgcolor = blue
1048#height = 5
1049#label density = 50
1050#bump = fast
1051#key = Reads HXB18 mirna
1052#category = microRNA
1053#
1054#[Coverage-HXB21-mirna]
1055#feature = coverage
1056#glyph = wiggle_xyplot
1057#database = HXB21-mirna
1058#height = 50
1059#fgcolor = black
1060#bgcolor = indigo
1061#key = Coverage HXB21 mirna
1062#category = microRNA
1063#label = 0
1064#
1065#[Reads-HXB21-mirna]
1066#feature = match
1067#glyph = segments
1068#draw_target = 1
1069#show_mismatch = 1
1070#mismatch_color = red
1071#database = HXB21-mirna
1072#bgcolor = blue
1073#fgcolor = blue
1074#height = 5
1075#label density = 50
1076#bump = fast
1077#key = Reads HXB21 mirna
1078#category = microRNA
1079#
1080#[Coverage-HXB23-mirna]
1081#feature = coverage
1082#glyph = wiggle_xyplot
1083#database = HXB23-mirna
1084#height = 50
1085#fgcolor = black
1086#bgcolor = indigo
1087#key = Coverage HXB23 mirna
1088#category = microRNA
1089#label = 0
1090#
1091#[Reads-HXB23-mirna]
1092#feature = match
1093#glyph = segments
1094#draw_target = 1
1095#show_mismatch = 1
1096#mismatch_color = red
1097#database = HXB23-mirna
1098#bgcolor = blue
1099#fgcolor = blue
1100#height = 5
1101#label density = 50
1102#bump = fast
1103#key = Reads HXB23 mirna
1104#category = microRNA
1105#
1106#[Coverage-HXB25-mirna]
1107#feature = coverage
1108#glyph = wiggle_xyplot
1109#database = HXB25-mirna
1110#height = 50
1111#fgcolor = black
1112#bgcolor = indigo
1113#key = Coverage HXB25 mirna
1114#category = microRNA
1115#label = 0
1116#
1117#[Reads-HXB25-mirna]
1118#feature = match
1119#glyph = segments
1120#draw_target = 1
1121#show_mismatch = 1
1122#mismatch_color = red
1123#database = HXB25-mirna
1124#bgcolor = blue
1125#fgcolor = blue
1126#height = 5
1127#label density = 50
1128#bump = fast
1129#key = Reads HXB25 mirna
1130#category = microRNA
1131#
1132#[Coverage-HXB29-mirna]
1133#feature = coverage
1134#glyph = wiggle_xyplot
1135#database = HXB29-mirna
1136#height = 50
1137#fgcolor = black
1138#bgcolor = indigo
1139#key = Coverage HXB29 mirna
1140#category = microRNA
1141#label = 0
1142#
1143#[Reads-HXB29-mirna]
1144#feature = match
1145#glyph = segments
1146#draw_target = 1
1147#show_mismatch = 1
1148#mismatch_color = red
1149#database = HXB29-mirna
1150#bgcolor = blue
1151#fgcolor = blue
1152#height = 5
1153#label density = 50
1154#bump = fast
1155#key = Reads HXB29 mirna
1156#category = microRNA
1157#
1158#[Coverage-SHR-mirna]
1159#feature = coverage
1160#glyph = wiggle_xyplot
1161#database = SHR-mirna
1162#height = 50
1163#fgcolor = black
1164#bgcolor = indigo
1165#key = Coverage SHR mirna
1166#category = microRNA
1167#label = 0
1168#
1169#[Reads-SHR-mirna]
1170#feature = match
1171#glyph = segments
1172#draw_target = 1
1173#show_mismatch = 1
1174#mismatch_color = red
1175#database = SHR-mirna
1176#bgcolor = blue
1177#fgcolor = blue
1178#height = 5
1179#label density = 50
1180#bump = fast
1181#key = Reads SHR mirna
1182#category = microRNA
1183
1184
1185
1186###############################################################################
1187###   Rbm20 track configurations
1188
1189#[Coverage-rbm20-mutant]
1190#feature = coverage
1191#glyph = wiggle_xyplot
1192#database = rbm20-mutant
1193#height = 50
1194#fgcolor = black
1195#bgcolor = indigo
1196#key = Coverage Rbm 20 mutant
1197#category = Rbm20 mRNA
1198#label = 0
1199#
1200#[Reads-rbm20-mutant]
1201#feature = match
1202#glyph = segments
1203#draw_target = 1
1204#show_mismatch = 1
1205#mismatch_color = red
1206#database = rbm20-mutant
1207#bgcolor = blue
1208#fgcolor = blue
1209#height = 5
1210#label density = 50
1211#bump = fast
1212#key = Reads Rbm 20 mutant
1213#category = Rbm20 mRNA
1214#
1215[Coverage-rbm20-wildtype]
1216feature = coverage
1217glyph = wiggle_xyplot
1218database = rbm20-wildtype
1219height = 50
1220fgcolor = black
1221bgcolor = indigo
1222key = Coverage BN
1223category = mRNA
1224label = 0
1225
1226[Reads-rbm20-wildtype]
1227feature = match
1228glyph = segments
1229draw_target = 1
1230show_mismatch = 1
1231mismatch_color = red
1232database = rbm20-wildtype
1233bgcolor = blue
1234fgcolor = blue
1235height = 5
1236label density = 50
1237bump = fast
1238key = Reads BN
1239category = mRNA
1240
1241[Reads-rbm20-wildtype-pairs]
1242feature       = read_pair
1243glyph         = segments
1244database      = rbm20-wildtype
1245draw_target   = 1
1246show_mismatch = 1
1247bgcolor       = sub {
1248                my $f = shift;
1249                return $f->attributes('M_UNMAPPED') ? 'red' : 'green';
1250                }
1251fgcolor       = green
1252height        = 3
1253label         = sub {shift->display_name}
1254label density = 50
1255bump          = fast
1256connector     = dashed
1257balloon hover = sub {
1258                my $f     = shift;
1259                return '' unless $f->type eq 'match';
1260                return 'Read: '.$f->display_name.' : '.$f->flag_str;
1261                }
1262key           = Read Pairs BN
1263category      = mRNA
1264
1265[rbm20_cluster]
1266feature       = experimental_feature:rbm20_clusters
1267database      = rbm20_cluster
1268glyph         = generic
1269bgcolor       = blue
1270fgcolor       = blue
1271forwardcolor  = blue
1272reversecolor  = blue
1273key           = Rbm20 cluster from human HEK cells
1274category      = Rbm20
1275
1276[rbm20_cufflinks_genes]
1277database     = rbm20_cluster
1278feature      = gene:Cufflinks
1279glyph        = gene
1280bgcolor      = dodgerblue
1281forwardcolor = dodgerblue
1282reversecolor = turquoise
1283label        = sub { my $f = shift;
1284                     my $name = $f->display_name;
1285                     my @aliases = sort $f->attributes('Alias');
1286                     $name .= " (@aliases)" if @aliases;
1287                     $name;
1288  }
1289height       = 6
1290description  = 0
1291key          = Cufflinks genes
1292category     = Rbm20
1293
1294
1295#
1296#
1297#[Coverage-rbm20-mutant-fwd]
1298#feature = coverage
1299#glyph = wiggle_xyplot
1300#database = rbm20-mutant-fwd
1301#height = 50
1302#fgcolor = black
1303#bgcolor = indigo
1304#key = Coverage Rbm 20 mutant fwd
1305#category = Rbm20 mRNA
1306#label = 0
1307#
1308#[Reads-rbm20-mutant-fwd]
1309#feature = match
1310#glyph = segments
1311#draw_target = 1
1312#show_mismatch = 1
1313#mismatch_color = red
1314#database = rbm20-mutant-fwd
1315#bgcolor = blue
1316#fgcolor = blue
1317#height = 5
1318#label density = 50
1319#bump = fast
1320#key = Reads Rbm 20 mutant fwd
1321#category = Rbm20 mRNA
1322#
1323#[Coverage-rbm20-wildtype-rev]
1324#feature = coverage
1325#glyph = wiggle_xyplot
1326#database = rbm20-wildtype-rev
1327#height = 50
1328#fgcolor = black
1329#bgcolor = indigo
1330#key = Coverage Rbm 20 wildtype rev
1331#category = Rbm20 mRNA
1332#label = 0
1333#
1334#[Reads-rbm20-wildtype-rev]
1335#feature = match
1336#glyph = segments
1337#draw_target = 1
1338#show_mismatch = 1
1339#mismatch_color = red
1340#database = rbm20-wildtype-rev
1341#bgcolor = blue
1342#fgcolor = blue
1343#height = 5
1344#label density = 50
1345#bump = fast
1346#key = Reads Rbm 20 wildtype rev
1347#category = Rbm20 mRNA
1348
1349
1350#[Coverage-wildtype2]
1351#feature        = solid:wildtype2-s14
1352#glyph          = wiggle_xyplot
1353#database       = rbm20
1354#height         = 50
1355#fgcolor        = black
1356#bgcolor        = indigo
1357#key            = Coverage wildtype 2
1358#category       = Rbm20 mRNA-seq
1359#label          = 0
1360
1361
1362
1363###############################################################################
1364###   Annotation track configurations
1365
1366
1367# microrna genes
1368[mirna-genes]
1369feature      = miRNA
1370database     = scaffolds
1371glyph        = generic
1372bgcolor      = red
1373forwardcolor = red
1374reversecolor = red
1375key          = mirbase microRNA
1376category     = microRNA
1377
1378
1379
1380# view deletions and snps
1381
1382[shr-deletions]
1383feature      = deletion:SHR
1384database     = variations
1385glyph        = generic
1386bgcolor      = red
1387forwardcolor = red
1388reversecolor = red
1389key          = SHR deletion
1390category     = Variations
1391
1392
1393[shr-SNPs]
1394feature       = SNP:SHR
1395database      = variations
1396glyph         = triangle
1397point         = 1
1398orient        = N
1399height        = 6
1400bgcolor       = blue
1401fgcolor       = blue
1402key           = SHR SNPs
1403category     = Variations
1404bump density  = 1
1405
1406#[shr-SNPs:100000]
1407#database      = variations
1408#feature       = snp_density
1409#glyph         = xyplot
1410#graph_type    = boxes
1411#scale         = right
1412
1413[hxb-sdp]
1414feature       = experimental_feature:hxb_sdp
1415database      = variations
1416glyph         = generic
1417bgcolor       = blue
1418fgcolor       = blue
1419forwardcolor  = blue
1420reversecolor  = blue
1421key           = BXH/HXB SDPs
1422category      = Variations
1423balloon click = <h2>Marker $name</h2>
1424       <a href='http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=$id'>Marker info from molgenis</a><br>
1425
1426
1427###
1428### This is a query by name:
1429### .../api/find/org.molgenis.xgap.Marker?name=1
1430
1431
1432[GC:region]
1433glyph        = dna
1434global feature = 1
1435database     = scaffolds
1436height       = 40
1437gc_window    = auto
1438do_gc        = 1
1439strand       = both
1440fgcolor      = red
1441axis_color   = blue
1442key          = GC Content
1443
1444[Genes]
1445feature      = gene:protein_coding
1446glyph        = gene
1447bgcolor      = dodgerblue
1448forwardcolor = dodgerblue
1449reversecolor = turquoise
1450label        = sub { my $f = shift;
1451                     my $name = $f->display_name;
1452                     my @aliases = sort $f->attributes('Alias');
1453                     $name .= " (@aliases)" if @aliases;
1454                     $name;
1455  }
1456height       = 6
1457description  = 0
1458key          = Ensembl genes
1459
1460
1461[Translation]
1462glyph        = translation
1463global feature = 1
1464database     = scaffolds
1465height       = 40
1466fgcolor      = purple
1467strand       = +1
1468translation  = 6frame
1469key          = 6-frame translation
1470
1471[TranslationF]
1472glyph        = translation
1473global feature = 1
1474database     = scaffolds
1475height       = 20
1476fgcolor      = purple
1477strand       = +1
1478translation  = 3frame
1479key          = 3-frame translation (forward)
1480
1481[DNA/GC Content]
1482glyph        = dna
1483global feature = 1
1484database     = scaffolds
1485height       = 40
1486do_gc        = 1
1487gc_window    = auto
1488strand       = both
1489fgcolor      = red
1490axis_color   = blue
1491
1492[TranslationR]
1493glyph        = translation
1494global feature = 1
1495database     = scaffolds
1496height       = 20
1497fgcolor      = blue
1498strand       = -1
1499translation  = 3frame
1500key          = 3-frame translation (reverse)