1b34ddd99f21b5b31c9c0b65ed7957fe29d29fb9
markd
  Tue Aug 19 10:21:11 2025 -0700
updates to recount3 tracks (not complete)

diff --git src/hg/makeDb/doc/hg38/recount3.txt src/hg/makeDb/doc/hg38/recount3.txt
index 9878eb2a15a..e7a19778d6c 100644
--- src/hg/makeDb/doc/hg38/recount3.txt
+++ src/hg/makeDb/doc/hg38/recount3.txt
@@ -1,39 +1,37 @@
 
 ####################################
 # recount3 intron tracks ticket 34886
 # Jeltje January 2025
 # NOTE: The sra files are so large that the trackDb.ra file needs a maxWindowToDraw limit
 # or else the browser window won't load within the set time
 
 see kent/src/hg/lib/recount3.as
 
 
 process_dataset() {
 	local dset=$1
 	if [ ! -f "$dset.tsv.bgz" ]; then
 	    wget -nv -O $dset.tsv.bgz https://snaptron.cs.jhu.edu/data/$dset/junctions.bgz
 	fi
         ~/kent/src/hg/makeDb/outside/recount3/junctionsToBed.py --junctions $dset.tsv.bgz --bed $dset.bed --decorator dec$dset.bed --compilation $dset
-	bedSort $dset.bed $dset.bed
-	bedSort dec$dset.bed dec$dset.bed
 }
 
 for dset in gtexv2 srav3h tcgav2 ccle; do
 	process_dataset $dset &
 done
 wait
 
 toBB() {
 	local dset=$1
 	bedToBigBed -type=bed9+6 -tab -as=${HOME}/kent/src/hg/lib/recount3.as $dset.bed /hive/data/genomes/hg38/chrom.sizes $dset.bb &
 	bedToBigBed -type=bed12+ -as=${HOME}/kent/src/hg/lib/decoration.as dec$dset.bed /hive/data/genomes/hg38/chrom.sizes dec$dset.bb &
 }
 
 for dset in gtexv2 srav3h tcgav2 ccle; do
 	toBB $dset &
 done
 wait
 
 rm *.bed *.tsv
 
 2025-08-04 markd: update to add size column for filter