Hi developers,
We all like your developing and maintaining KentUtils as a convenient and useful tools for genomic study and analysis. However it seems there is still some issue about some of the tools for me right now.
I followed the Whole_genome_alignment_howto pipeline to generate a home-made WGA, and for some reason I converted Chain to Psl, and converted back using ChainToPsl and PslToChain. It works ok for forward strand chains, while not for reserved strand.
For example,
one of my raw chain:
after converted to psl and coverted back, my converted chain:
it seems the qstart and qend coordinates are not listed in terms of the reverse-complemented sequence.
my util version is v385 downloaded from genomebrowser and the commands are:
~/softwares/KentUtilities-linux.x86_64.v385/chainToPsl ./all.chain tSizes qSizes target.fa query.fa ./all.psl
~/softwares/KentUtilities-linux.x86_64.v385/pslToChain ./all.psl ./all.psl.chain
Is it the utilities designed so or my mistake using?
Many Thanks for your help
Yours sincerely,
Hao
Hello, Hao.
We have not heard from you. We wanted to follow up and see if the problem was resolved.
If not, could you provide us with a URL to the files you are using for conversion so we can try the conversion here?
If you don't want to share this information with our publicly-archived mailing list (gen...@soe.ucsc.edu), you can send it to our confidential support list at genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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