
####################################
# 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
}

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
