[GENERAL] description = Rattus norvegicus database = scaffolds initial landmark = chr19:143000..180000 default tracks = Genes # examples to show in the introduction examples = chr1 chr1:80,000..120,000 # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ID # try to configure the rubberband menu to query for eQTLs [DETAIL SELECT MENU] width = 250 html =
SELECTION [X]
Zoom in
Recenter on this region
Dump selection as FASTA
eQTL markers in selection
eQTL transcripts in selection
cis eQTLs in selection
coding SNPs in selection
molgenis region query
### ### The last entry in the menu list is a molgenis example which creates urls: ### .../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999 ################################# # database definitions ################################# [scaffolds:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=rn4 -user apache [variations:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=rn4_variations -user apache # for the SNP density plots aggregators = snp_density{bin:SNP:SHR} ############################################################################### ### Rbm 20 databasese [rbm20_cluster:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=rn4_rbm20_cluster -user apache # [rbm20:database] # db_adaptor = Bio::DB::SeqFeature::Store # db_args = -adaptor DBI::mysql # -dsn dbi:mysql:database=rn4_rbm20 # -user apache #[rbm20-mutant:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam #search options = default # [rbm20-wildtype:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/rbm20/wildtype.bam search options = default #[rbm20-mutant-fwd:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam #search options = default # #[rbm20-wildtype-fwd:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam #search options = default # #[rbm20-mutant-rev:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam #search options = default # #[rbm20-wildtype-rev:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam #search options = default ############################################################################### ### histone modification databases [histones:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=rn4_histones -user apache [histones_h3k27me3:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=rn4_histones_h3k27me3 -user apache # [lv-H3K4me3-BN-male-bio2-tech1:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-male-bio2-tech1-rmdup.bam [lv-H3K4me3-SHR-male-bio2-tech1:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-male-bio2-tech1-rmdup.bam [lv-H3K4me3-BN-female-bio1-tech1:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-female-bio1-tech1-rmdup.bam [lv-H3K4me3-SHR-female-bio1-tech1:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-female-bio1-tech1-rmdup.bam [lv-H3K27me3-BN-male-bio2-merged:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio2-merged.bam [lv-H3K27me3-BN-male-bio3-merged:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio3-merged.bam [lv-H3K27me3-BN-male-bio4-merged:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio4-merged.bam [BN-H3K4me3:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K4me3-sorted.bam search options = default [BN-H3K27me3:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K27me3-sorted.bam search options = default [BN-input:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-input-sorted.bam search options = default [SHR-H3K4me3:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K4me3-sorted.bam search options = default [SHR-H3K27me3:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K27me3-sorted.bam search options = default [SHR-input:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-input-sorted.bam search options = default [BXH12-H3K4:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH12_sorted.bam search options = default [BXH02-H3K4:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH02_sorted.bam search options = default [BXH03-H3K4:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH03.bam search options = default ############################################################################### ### micro rna databases [BN-mirna:database] db_adaptor = Bio::DB::Sam db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa -bam /var/www/html/gbrowse2/databases/rn4/mirna/BN.csfasta__sorted.bam search options = default #[HXB01-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB01.csfasta__sorted.bam #search options = default #[HXB03-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB03.csfasta__sorted.bam #search options = default #[HXB05-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB05.csfasta__sorted.bam #search options = default #[HXB10-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB10.csfasta__sorted.bam #search options = default #[HXB15-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB15.csfasta__sorted.bam #search options = default #[HXB18-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB18.csfasta__sorted.bam #search options = default #[HXB21-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB21.csfasta__sorted.bam #search options = default #[HXB23-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB23.csfasta__sorted.bam #search options = default #[HXB25-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB25.csfasta__sorted.bam #search options = default #[HXB29-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB29.csfasta__sorted.bam #search options = default #[SHR-mirna:database] #db_adaptor = Bio::DB::Sam #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa #-bam /var/www/html/gbrowse2/databases/rn4/mirna/SHR.csfasta__sorted.bam #search options = default ############################################################################### ### track configurations # Default glyph settings [TRACK DEFAULTS] glyph = generic database = scaffolds height = 8 bgcolor = cyan fgcolor = black label density = 25 bump density = 100 ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks # view the reads ############################################################################### ### histone modifications track configurations # for the sex specific analysis [Coverage-lv-H3K4me3-BN-female-bio1-tech1] feature = coverage glyph = wiggle_xyplot database = lv-H3K4me3-BN-female-bio1-tech1 height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K4me3-BN-female-bio1-tech1 category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [Coverage-lv-H3K4me3-SHR-female-bio1-tech1] feature = coverage glyph = wiggle_xyplot database = lv-H3K4me3-SHR-female-bio1-tech1 height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K4me3-SHR-female-bio1-tech1 category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [lv-H3K4me3-BN-male-bio2-tech1] feature = coverage glyph = wiggle_xyplot database = lv-H3K4me3-BN-male-bio2-tech1 height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K4me3-BN-male-bio2-tech1 category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [lv-H3K4me3-SHR-male-bio2-tech1-rmdup] feature = coverage glyph = wiggle_xyplot database = lv-H3K4me3-SHR-male-bio2-tech1 height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K4me3-SHR-male-bio2-tech1 category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. # BN [Coverage-lv-H3K27me3-BN-male-bio2-merged] feature = coverage glyph = wiggle_xyplot database = lv-H3K27me3-BN-male-bio2-merged height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K27me3-BN-male-bio2-merged category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [Coverage-lv-H3K27me3-BN-male-bio3-merged] feature = coverage glyph = wiggle_xyplot database = lv-H3K27me3-BN-male-bio3-merged height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K27me3-BN-male-bio3-merged category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [Coverage-lv-H3K27me3-BN-male-bio4-merged] feature = coverage glyph = wiggle_xyplot database = lv-H3K27me3-BN-male-bio4-merged height = 50 fgcolor = black bgcolor = indigo key = Coverage lv-H3K27me3-BN-male-bio4-merged category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [Coverage-BN-H3K4me3] feature = coverage glyph = wiggle_xyplot database = BN-H3K4me3 height = 50 fgcolor = black bgcolor = indigo key = Coverage BN-H3K4me3 category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. # [Coverage-BN-H3K27me3] # feature = coverage # glyph = wiggle_xyplot # database = BN-H3K27me3 # height = 50 # fgcolor = black # bgcolor = indigo # key = Coverage BN-H3K27me3 # category = Histone modifications # label = 0 # Labels on wiggle tracks are redundant. [Coverage-BN-input] feature = coverage glyph = wiggle_xyplot database = BN-input height = 50 fgcolor = black bgcolor = indigo key = Coverage BN-input category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. # [Reads-BN-H3K4me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = BN-H3K4me3 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads BN-H3K4me3 # category = Histone modifications # # [Reads-BN-H3K27me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = BN-H3K27me3 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads BN-H3K27me3 # category = Histone modifications # # [Reads-BN-input] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = BN-input # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads BN-input # category = Histone modifications # SHR reads [Coverage-SHR-H3K4me3] feature = coverage glyph = wiggle_xyplot database = SHR-H3K4me3 height = 50 fgcolor = black bgcolor = indigo key = Coverage SHR-H3K4me3 category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. [Coverage-SHR-input] feature = coverage glyph = wiggle_xyplot database = SHR-input height = 50 fgcolor = black bgcolor = indigo key = Coverage SHR-input category = Histone modifications label = 0 # Labels on wiggle tracks are redundant. # [Reads-SHR-H3K4me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = SHR-H3K4me3 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads SHR-H3K4me3 # category = Histone modifications # # [Reads-SHR-H3K27me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = SHR-H3K27me3 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads SHR-H3K27me3 # category = Histone modifications # # [Reads-SHR-input] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = SHR-input # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads SHR-input # category = Histone modifications # # # # reads for the RI strains # [Coverage-BXH12-H3K4me3] # feature = coverage # glyph = wiggle_xyplot # database = BXH12-H3K4 # height = 50 # fgcolor = black # bgcolor = indigo # key = Coverage BXH12-H3K4 # category = Histone modifications # label = 0 # Labels on wiggle tracks are redundant. # # [Reads-BXH12-H3K4me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = BXH12-H3K4 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads BXH12-H3K4me3 # category = Histone modifications # # # [Coverage-BXH02-H3K4me3] # feature = coverage # glyph = wiggle_xyplot # database = BXH02-H3K4 # height = 50 # fgcolor = black # bgcolor = indigo # key = Coverage BXH102-H3K4 # category = Histone modifications # label = 0 # Labels on wiggle tracks are redundant. # # [Reads-BXH02-H3K4me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = BXH02-H3K4 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads BXH02-H3K4me3 # category = Histone modifications # # [Coverage-BXH03-H3K4me3] # feature = coverage # glyph = wiggle_xyplot # database = BXH03-H3K4 # height = 50 # fgcolor = black # bgcolor = indigo # key = Coverage BXH103-H3K4 # category = Histone modifications # label = 0 # Labels on wiggle tracks are redundant. # # # [Reads-BXH03-H3K4me3] # feature = match # glyph = segments # draw_target = 1 # show_mismatch = 1 # mismatch_color = red # database = BXH03-H3K4 # bgcolor = blue # fgcolor = blue # height = 5 # label density = 50 # bump = fast # key = Reads BXH03-H3K4me3 # category = Histone modifications # # # # view the results of the island calling and differential analysis # [sicer-BN-H3K4me3] # feature = experimental_feature:sicer-BN-H3K4me3 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer BN-H3K4me3 # category = Histone modifications # # [sicer-BN-H3K27me3] # feature = experimental_feature:sicer-BN-H3K27me3 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer BN-H3K27me3 # category = Histone modifications # # [sicer-BN-input] # feature = experimental_feature:sicer-BN-input # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer BN-input # category = Histone modifications # # [sicer-SHR-H3K4me3] # feature = experimental_feature:sicer-SHR-H3K4me3 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer SHR-H3K4me3 # category = Histone modifications # # [sicer-SHR-H3K27me3] # feature = experimental_feature:sicer-SHR-H3K27me3 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer SHR-H3K27me3 # category = Histone modifications # # [sicer-SHR-input] # feature = experimental_feature:sicer-SHR-input # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer SHR-input # category = Histone modifications # # [chipdiff-H3K4me3] # feature = experimental_feature:chipdiff-H3K4me3 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Chipdiff H3K4me3 # category = Histone modifications # # [chipdiff-H3K27me3] # feature = experimental_feature:chipdiff-H3K27me3 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Chipdiff H3K27me3 # category = Histone modifications # # # # tracks for the peak calls in the RI strains # [sicer-H3K4-BXH02] # feature = experimental_feature:sicer-K4-BXH02 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer H3K4 BXH02 # category = Histone modifications # # # [sicer-H3K4-BXH12] # feature = experimental_feature:sicer-K4-BXH12 # database = histones # glyph = generic # bgcolor = red # forwardcolor = red # reversecolor = red # key = Sicer H3K4 BXH12 # category = Histone modifications # ############################################################################### ### Binned H3K27me3 data # [binned-lv-H3K27me3-BN-male-bio4-merged-offset-3750] # feature = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750 # database = histones_h3k27me3 # glyph = wiggle_xyplot # smoothing = none # autoscale = local # bgcolor = indigo # height = 50 # graph_type = boxes # scale = right # description = 1 # category = Binned H3k27me3 data # key = lv-H3K27me3-BN-male-bio4-merged-offset-3750 # # [posterior-lv-H3K27me3-BN-male-bio4-merged-offset-3750] # feature = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm # database = histones_h3k27me3 # glyph = wiggle_xyplot # smoothing = none # autoscale = global # bicolor_pivot = 0.99 # pos_color = red # neg_color = gray # height = 25 # graph_type = boxes # scale = right # description = 1 # category = Binned H3k27me3 data # key = lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm #[binned-binsize-5000-posterior-lv-H3K27me3-BN-male-bio2-merged-avg-posterior] #feature = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-avg-posterior-binsize-5000 #database = histones_h3k27me3 #glyph = wiggle_xyplot #smoothing = none #autoscale = global #bicolor_pivot = 0.99 #pos_color = red #neg_color = gray #height = 25 #graph_type = boxes #scale = right #description = 1 #category = Binned H3k27me3 data #key = lv-H3K27me3-BN-male-bio2-merged-hmm-avg-binsize-5000 # # [binned-binsize-3000-posterior-lv-H3K27me3-BN-male-bio2-merged-offset-0-posterior] feature = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000 database = histones_h3k27me3 glyph = wiggle_xyplot smoothing = none autoscale = global bicolor_pivot = 0.99 pos_color = red neg_color = gray height = 25 graph_type = boxes scale = right description = 1 category = Binned H3k27me3 data key = lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000 #include "/project/intranet/gbrowse2/databases/rn4/histone-modifications/binned-data/binned-data.conf" ############################################################################### ### microrna track configurations [Coverage-BN-mirna] feature = coverage glyph = wiggle_xyplot database = BN-mirna height = 50 fgcolor = black bgcolor = indigo key = Coverage BN mirna category = microRNA label = 0 # Labels on wiggle tracks are redundant. [Reads-BN-mirna] feature = match glyph = segments draw_target = 1 show_mismatch = 1 mismatch_color = red database = BN-mirna bgcolor = blue fgcolor = blue height = 5 label density = 50 bump = fast key = Reads BN mirna category = microRNA #[Coverage-HXB01-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB01-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB01 mirna #category = microRNA #label = 0 # #[Reads-HXB01-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB01-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB01 mirna #category = microRNA # #[Coverage-HXB03-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB03-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB03 mirna #category = microRNA #label = 0 # #[Reads-HXB03-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB03-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB03 mirna #category = microRNA # #[Coverage-HXB05-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB05-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB05 mirna #category = microRNA #label = 0 # #[Reads-HXB05-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB05-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB05 mirna #category = microRNA # #[Coverage-HXB10-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB10-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB10 mirna #category = microRNA #label = 0 # #[Reads-HXB10-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB10-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB10 mirna #category = microRNA # #[Coverage-HXB15-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB15-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB15 mirna #category = microRNA #label = 0 # #[Reads-HXB15-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB15-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB15 mirna #category = microRNA # #[Coverage-HXB18-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB18-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB18 mirna #category = microRNA #label = 0 # #[Reads-HXB18-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB18-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB18 mirna #category = microRNA # #[Coverage-HXB21-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB21-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB21 mirna #category = microRNA #label = 0 # #[Reads-HXB21-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB21-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB21 mirna #category = microRNA # #[Coverage-HXB23-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB23-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB23 mirna #category = microRNA #label = 0 # #[Reads-HXB23-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB23-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB23 mirna #category = microRNA # #[Coverage-HXB25-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB25-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB25 mirna #category = microRNA #label = 0 # #[Reads-HXB25-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB25-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB25 mirna #category = microRNA # #[Coverage-HXB29-mirna] #feature = coverage #glyph = wiggle_xyplot #database = HXB29-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage HXB29 mirna #category = microRNA #label = 0 # #[Reads-HXB29-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = HXB29-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads HXB29 mirna #category = microRNA # #[Coverage-SHR-mirna] #feature = coverage #glyph = wiggle_xyplot #database = SHR-mirna #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage SHR mirna #category = microRNA #label = 0 # #[Reads-SHR-mirna] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = SHR-mirna #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads SHR mirna #category = microRNA ############################################################################### ### Rbm20 track configurations #[Coverage-rbm20-mutant] #feature = coverage #glyph = wiggle_xyplot #database = rbm20-mutant #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage Rbm 20 mutant #category = Rbm20 mRNA #label = 0 # #[Reads-rbm20-mutant] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = rbm20-mutant #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads Rbm 20 mutant #category = Rbm20 mRNA # [Coverage-rbm20-wildtype] feature = coverage glyph = wiggle_xyplot database = rbm20-wildtype height = 50 fgcolor = black bgcolor = indigo key = Coverage BN category = mRNA label = 0 [Reads-rbm20-wildtype] feature = match glyph = segments draw_target = 1 show_mismatch = 1 mismatch_color = red database = rbm20-wildtype bgcolor = blue fgcolor = blue height = 5 label density = 50 bump = fast key = Reads BN category = mRNA [Reads-rbm20-wildtype-pairs] feature = read_pair glyph = segments database = rbm20-wildtype draw_target = 1 show_mismatch = 1 bgcolor = sub { my $f = shift; return $f->attributes('M_UNMAPPED') ? 'red' : 'green'; } fgcolor = green height = 3 label = sub {shift->display_name} label density = 50 bump = fast connector = dashed balloon hover = sub { my $f = shift; return '' unless $f->type eq 'match'; return 'Read: '.$f->display_name.' : '.$f->flag_str; } key = Read Pairs BN category = mRNA [rbm20_cluster] feature = experimental_feature:rbm20_clusters database = rbm20_cluster glyph = generic bgcolor = blue fgcolor = blue forwardcolor = blue reversecolor = blue key = Rbm20 cluster from human HEK cells category = Rbm20 [rbm20_cufflinks_genes] database = rbm20_cluster feature = gene:Cufflinks glyph = gene bgcolor = dodgerblue forwardcolor = dodgerblue reversecolor = turquoise label = sub { my $f = shift; my $name = $f->display_name; my @aliases = sort $f->attributes('Alias'); $name .= " (@aliases)" if @aliases; $name; } height = 6 description = 0 key = Cufflinks genes category = Rbm20 # # #[Coverage-rbm20-mutant-fwd] #feature = coverage #glyph = wiggle_xyplot #database = rbm20-mutant-fwd #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage Rbm 20 mutant fwd #category = Rbm20 mRNA #label = 0 # #[Reads-rbm20-mutant-fwd] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = rbm20-mutant-fwd #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads Rbm 20 mutant fwd #category = Rbm20 mRNA # #[Coverage-rbm20-wildtype-rev] #feature = coverage #glyph = wiggle_xyplot #database = rbm20-wildtype-rev #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage Rbm 20 wildtype rev #category = Rbm20 mRNA #label = 0 # #[Reads-rbm20-wildtype-rev] #feature = match #glyph = segments #draw_target = 1 #show_mismatch = 1 #mismatch_color = red #database = rbm20-wildtype-rev #bgcolor = blue #fgcolor = blue #height = 5 #label density = 50 #bump = fast #key = Reads Rbm 20 wildtype rev #category = Rbm20 mRNA #[Coverage-wildtype2] #feature = solid:wildtype2-s14 #glyph = wiggle_xyplot #database = rbm20 #height = 50 #fgcolor = black #bgcolor = indigo #key = Coverage wildtype 2 #category = Rbm20 mRNA-seq #label = 0 ############################################################################### ### Annotation track configurations # microrna genes [mirna-genes] feature = miRNA database = scaffolds glyph = generic bgcolor = red forwardcolor = red reversecolor = red key = mirbase microRNA category = microRNA # view deletions and snps [shr-deletions] feature = deletion:SHR database = variations glyph = generic bgcolor = red forwardcolor = red reversecolor = red key = SHR deletion category = Variations [shr-SNPs] feature = SNP:SHR database = variations glyph = triangle point = 1 orient = N height = 6 bgcolor = blue fgcolor = blue key = SHR SNPs category = Variations bump density = 1 #[shr-SNPs:100000] #database = variations #feature = snp_density #glyph = xyplot #graph_type = boxes #scale = right [hxb-sdp] feature = experimental_feature:hxb_sdp database = variations glyph = generic bgcolor = blue fgcolor = blue forwardcolor = blue reversecolor = blue key = BXH/HXB SDPs category = Variations balloon click =

Marker $name

Marker info from molgenis
### ### This is a query by name: ### .../api/find/org.molgenis.xgap.Marker?name=1 [GC:region] glyph = dna global feature = 1 database = scaffolds height = 40 gc_window = auto do_gc = 1 strand = both fgcolor = red axis_color = blue key = GC Content [Genes] feature = gene:protein_coding glyph = gene bgcolor = dodgerblue forwardcolor = dodgerblue reversecolor = turquoise label = sub { my $f = shift; my $name = $f->display_name; my @aliases = sort $f->attributes('Alias'); $name .= " (@aliases)" if @aliases; $name; } height = 6 description = 0 key = Ensembl genes [Translation] glyph = translation global feature = 1 database = scaffolds height = 40 fgcolor = purple strand = +1 translation = 6frame key = 6-frame translation [TranslationF] glyph = translation global feature = 1 database = scaffolds height = 20 fgcolor = purple strand = +1 translation = 3frame key = 3-frame translation (forward) [DNA/GC Content] glyph = dna global feature = 1 database = scaffolds height = 40 do_gc = 1 gc_window = auto strand = both fgcolor = red axis_color = blue [TranslationR] glyph = translation global feature = 1 database = scaffolds height = 20 fgcolor = blue strand = -1 translation = 3frame key = 3-frame translation (reverse)