66604eefdbb0971ed43ee81bd6f18cc3a409e304
markd
  Sat Jan 10 13:18:44 2026 -0800
color-code clsLongReadRna modles (#36908)

diff --git src/hg/makeDb/doc/mm10.clsLongReadRna.txt src/hg/makeDb/doc/mm10.clsLongReadRna.txt
index cb8dd85a23f..8dab04f1c41 100644
--- src/hg/makeDb/doc/mm10.clsLongReadRna.txt
+++ src/hg/makeDb/doc/mm10.clsLongReadRna.txt
@@ -1,66 +1,90 @@
 ####
 # 2025-06-07 CLS long-read RNA  (Mark Diekhans <markd@ucsc.edu>)
 #
 # See also hg38/clsLongReadRna.txt
 ####
 
 clsSrc=$HOME/compbio/browser/dev/kent/src/hg/makeDb/outside/clsLongReadRna
 clsTrackTool=${clsSrc}/clsTrackTool
 clsModelBedAs=${clsSrc}/clsModelBed.as 
 clsTargetBedAs=${clsSrc}/clsTargetBed.as
 gff_attrs_extract=${clsSrc}/gff-attrs-extract.awk
 
 cd /hive/data/genomes/mm10/bed/clsLongReadRna
 
 # Obtained human and mouse BAMs and indexes
   https://public-docs.crg.es/rguigo/Data/scarbonell/gencode_paper2024_figures/browser_tracks/hub/path2LyRicBAMs.tsv 
 
   copy BAMs directly from CRG via my account, split BAMs into pre-capture and
   post-capture directories
 
 
 # download LyRic models and metadata:
   metadata documented here:
   https://github.com/guigolab/gencode-cls-master-table
   cd lyric-data
   wget -nv https://github.com/guigolab/gencode-cls-master-table/releases/latest/download/Mv2_masterTable_refined.gtf.gz
   wget -nv https://github.com/guigolab/gencode-cls-master-table/releases/download/GencodeCLS_v1.0/Mv2_metadata.tsv.gz
   wget -nv https://github.com/guigolab/gencode-cls-master-table/releases/download/Supplementary/Mv2_CLS3_targetDesign_mergedRegions.gtf.gz
 
 # check BAMs vs metadata
   $clsTrackTool check-bams lyric-data/Mv2_metadata.tsv.gz .
 
 # process GTF
   # convert to BED via GTF -> GFF3 -> genePred -> BED
   # need to go via GFF3 to get attributes in a file
   cd lyric-data/
   zcat Mv2_masterTable_refined.gtf.gz | gffread -F | gff3ToGenePred -attrsOut=Mv2_masterTable_refined.attrs.tab stdin stdout |\
     genePredToBed stdin stdout | tawk '{$7=$2; print}' | sort -k1,1 -k2,2n |gzip -9 > Mv2_masterTable_refined.bed.gz 
 
   # extract tags of interest to  TSV
   tawk -f  $gff_attrs_extract Mv2_masterTable_refined.attrs.tab |pigz -c  >Mv2_transcript-meta.tsv.gz
   rm Mv2_masterTable_refined.attrs.tab
 
   # build target BEDs (discards ERCC-0* entries)
   zcat Mv2_CLS3_targetDesign_mergedRegions.gtf.gz | ../../target-gff-to-bed | pigz -c  >../cls-targets.bed.gz
 
 # make model BEDs
   one for each sample+phase+platform,
   one for each sample
   one with all
 
   $clsTrackTool make-beds lyric-data/Mv2_metadata.tsv.gz lyric-data/Mv2_masterTable_refined.bed.gz lyric-data/Mv2_transcript-meta.tsv.gz . &
   bedToBigBed -tab -type=bed6+2 -as=$clsTargetBedAs -sizesIsChromAliasBb cls-targets.bed.gz /hive/data/genomes/mm10/bed/chromAlias/p6/mm10.chromAlias.bb cls-targets.bb
   for bed in cls-models*.bed.gz cls-models.bed.gz *capture/*.bed.gz ; do
      bedToBigBed -tab -type=bed12+3 -as=$clsModelBedAs -sizesIsChromAliasBb $bed /hive/data/genomes/mm10/bed/chromAlias/p6/mm10.chromAlias.bb $(dirname $bed)/$(basename $bed .bed.gz).bb
   done
 
 # make trackDb
   $clsTrackTool make-trackdb --parent=long_read_transcripts lyric-data/Mv2_metadata.tsv.gz /gbdb/mm10/clsLongReadRna ~/kent/src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra
 
   # edit to make member of long_read_transcripts.ra:
     include clsLongReadRna.ra alpha
 
 # link to gbdb
   mkdir -p /gbdb/mm10/clsLongReadRna/{post-capture,pre-capture}
   for bb in $(find . -name '*.bb' -o  -name '*.bam*') ; do ln -sf $(realpath $bb) /gbdb/mm10/clsLongReadRna/$bb ; done
+
+# 2026-01-09 markd
+  Based on paper review feedback, adding color coding and filters to indicate if 
+  transcript model was added to GENCODE and if so, indicate the assigned transcript
+  type.
+
+  # obtain mappings
+    https://github.com/guigolab/cls3-final-files-description?tab=readme-ov-file#v47-CLS3-Mappings-detailed
+
+    cd lyric-data
+    wget -nv https://public-docs.crg.es/rguigo/Data/gkaur/CLS3_finalFiles/v47-CLS3mapping_status.txthttps://public-docs.crg.es/rguigo/Data/gkaur/CLS3_finalFiles/vM36-CLS3mapping_status.txt
+    pigz vM36-CLS3mapping_status.txt
+    cd ..
+
+   # generate BEDS
+   $clsTrackTool make-beds lyric-data/Mv2_metadata.tsv.gz lyric-data/Mv2_masterTable_refined.bed.gz lyric-data/Mv2_transcript-meta.tsv.gz lyric-data/vM36-CLS3mapping_status.txt.gz . &
+    Note: 539 or 282296 models are mapped to multiple GENCODE transcripts
+
+   for bed in cls-models*.bed.gz cls-models.bed.gz *capture/*.bed.gz ; do
+     (bedToBigBed -tab -type=bed12+3 -as=$clsModelBedAs -sizesIsChromAliasBb $bed /hive/data/genomes/mm10/bed/chromAlias/p6/mm10.chromAlias.bb $(dirname $bed)/$(basename $bed .bed.gz).bb &)
+   done
+
+  # make trackDb
+  $clsTrackTool make-trackdb --parent=long_read_transcripts lyric-data/Mv2_metadata.tsv.gz /gbdb/mm10/clsLongReadRna ~/kent/src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra