Request three chain files for cross-species alignment

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Jinll

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Aug 9, 2024, 6:27:34 PM8/9/24
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Dear UCSC Genome Browser support,

 

I hope this email finds you in good health and thank you for the work that you are doing. I am trying to view the homologous sequences of BED generated using the cattle reference genome ARS-UCD1.2 to three other species: pig (Sscrofa11.1), horse (EquCab3.0) and sheep (ARS-UI_Ramb_v3.0). However, I am unable to find the appropriate chain file on the UCSC Genome Browser website.

 

I tried to manually create chain files according to the pipeline (https://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl), but Parasol did not work very well, especially since I don't have ROOT access and can't solve the problem well.

 

Therefore, I was wondering if it would be possible to provide three chain files: cattle2pig.chain, cattle2horse.chain and cattle2sheep.chain, and it would be better to add support for other task submission systems (e.g. PBS,QSUB,JSUB, etc.).

 

Thank you for your time and I look forward to hearing from you.

 

Kind regards,

Leon.


Luis Nassar

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Aug 9, 2024, 6:42:34 PM8/9/24
to Jinll, gen...@soe.ucsc.edu

Hello, Leon.

We are running up those 3 liftOver files now. They take a few days, so we will send you a follow-up email when they are done.

You are not alone in your difficulties in running the liftOver pipeline. It was designed in-house and the parasol batch system was also entirely written in-house, so adapting it for general use can be troublesome. Thank you for the suggestions, we will keep them in mind. In the meantime, let us know if you require additional files and we can run them up for you.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute


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Luis Nassar

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Aug 14, 2024, 11:16:59 PM8/14/24
to Jinll, gen...@soe.ucsc.edu
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