#DONE braney 2022-02-12

mkdir -p /cluster/data/hg38/bed/mane.1.0
cd /cluster/data/hg38/bed/mane.1.0

bigBedToBed https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_1.0/MANE.GRCh38.v1.0.ensembl.bb our.bed

bedToBigBed -extraIndex=name our.bed /cluster/data/hg38/chrom.sizes our.bb -type=bed12+13 -as=$HOME/kent/src/hg/lib/mane.as -tab
mkdir -p /gbdb/hg38/mane
rm -f /gbdb/hg38/mane/mane.1.0.bb
ln -s `pwd`/our.bb /gbdb/hg38/mane/mane.1.0.bb

tawk '{print $13, $18, $19, $21, $22, $23, $24}' our.bed > our.ixInput
ixIxx our.ixInput mane.1.0.ix mane.1.0.ixx
rm -f /gbdb/hg38/mane/mane.1.0.ix /gbdb/hg38/mane/mane.1.0.ixx
ln -s `pwd`/mane.1.0.ix /gbdb/hg38/mane
ln -s `pwd`/mane.1.0.ixx /gbdb/hg38/mane