dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a braney Tue Apr 22 12:26:11 2025 -0700 sessions save a copy of the quickLift hub. diff --git src/hg/makeDb/doc/bosTau9/genarkQuickLift.txt src/hg/makeDb/doc/bosTau9/genarkQuickLift.txt new file mode 100644 index 00000000000..38120189636 --- /dev/null +++ src/hg/makeDb/doc/bosTau9/genarkQuickLift.txt @@ -0,0 +1,26 @@ +mkdir -p /hive/data/genomes/bosTau9/bed/quickLift +cd /hive/data/genomes/bosTau9/bed/quickLift + +zcat /gbdb/bosTau9/liftOver/bosTau9ToGCF_002263795.3.over.chain.gz | chainSwap stdin over.swap.chain + + awk '/chain/ {print $3, $4}' over.swap.chain | sort | uniq > size.txt + +i=GCF_002263795.3 +hgLoadChain -noBin -test bosTau9 bigChain over.swap.chain +sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > tmp.bigChain +bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab tmp.bigChain size.txt $i.bb +awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n > tmp.bigChain.bigLink +bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab tmp.bigChain.bigLink size.txt $i.link.bb + +i=GCF_002263795.3.link.bb +mkdir -p /gbdb/bosTau9/quickLift +rm tableData.txt +s=`basename $i .link.bb`.bb +db=`basename $s .bb` +f=/gbdb/bosTau9/quickLift/$s +g=/gbdb/bosTau9/quickLift/$i +echo ln -s `pwd`/$s $f +echo ln -s `pwd`/$i $g +echo "0 bosTau9 $db $f" | tr ' ' '\t' >> tableData.txt + +hgLoadSqlTab -append hgcentraltest quickLiftChain $HOME/kent/src/hg/lib/quickLiftChain.sql tableData.txt