Closed gsc74 closed 1 year ago
@milkschen and @nhansen, I'm using the following command to generate
liftover-split.paf
python3 chaintools/src/chaintools/to_paf.py -c liftover-split.chain -t ../CHM13Y_L.fa -q ../GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta -o liftover-split.paf
It seems that generating
*.paf
fromto_paf.py
is very slow. What is the alternate way to speed up the computation? And what is the estimated time for whole genome human references?
Target and query sequences were interchanged, and that was the issue.
Hi @gsc74, Thanks for sharing the experience!
@milkschen and @nhansen, I'm using the following command to generate
liftover-split.paf
It seems that generating
*.paf
fromto_paf.py
is very slow. What is the alternate way to speed up the computation? And what is the estimated time for whole genome human references?