issue about KentUtils ChainToPsl and PslToChain

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YUAN Hao

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Sep 15, 2022, 2:01:05 AM9/15/22
to gen...@soe.ucsc.edu

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

Hiram Clawson

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Sep 15, 2022, 2:39:57 AM9/15/22
to YUAN Hao, gen...@soe.ucsc.edu
Good Evening Hao:

I can not reproduce this issue with the v385 versions of the commands or
with the current version of the commands.

v385 binaries:

-rwxrwxr-x 1 5234032 Dec 12 2019 chainToPsl
-rwxrwxr-x 1 5295904 Dec 12 2019 pslToChain

Can you provide a URL to the files you are using for conversion so I can
try the conversion here ? The inputs: all.chain tSizes qSizes target.fa query.fa

I compared the 'chain' lines in the original file before to the resulting
chain file after:

zgrep -v "^#" all.chain.gz | grep -w chain | cut -d' ' -f3- | sort > initial.chain.lines

grep -v "^#" back.to.chain | grep -w chain | cut -d' ' -f3- | sort > back.to.chain.lines

md5sum back.to.chain.lines initial.chain.lines

7af0a0c160789d5a5c616a4b118c5585 back.to.chain.lines
7af0a0c160789d5a5c616a4b118c5585 initial.chain.lines

--Hiram

On 9/14/22 9:35 PM, YUAN Hao wrote:
> 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:
>

Gerardo Perez

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Sep 23, 2022, 1:28:23 PM9/23/22
to YUAN Hao, gen...@soe.ucsc.edu, Hiram Clawson

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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