Request chain of goat ARS1 (GCA_001704415.1) assembly

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汪富文

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Aug 12, 2024, 6:01:20 PM8/12/24
to genome
Dear UCSC Genome Browser group,
Thank you very much for your team's vital support for the scientific research work. I'm studying goat (ARS1, GCA_001704415.1)  mammary and trying to compare it to mouse(GRCm39,GCA_000001635.9) and pig (Sscrofa11.1, GCA_000003025.6), and hope your team can help us on creating chain file.
In fact, I've been trying to create a chain file for a week. I followed the pipeline(DoBlastzChainNet.pl - genomewiki (ucsc.edu)) and run the task successfully.My script is as follows:
export PATH="/storage/reference/13.cross.species/01.create.chain/bin:$PATH"
faToTwoBit /storage/reference/10.goat/Capra_hircus.ARS1.dna.toplevel.fa Capra_hircus.ARS1.dna.toplevel.2bit
twoBitInfo Capra_hircus.ARS1.dna.toplevel.2bit stdout | sort -k2,2nr > Capra_hircus.ARS1.dna.toplevel.chrom.sizes
faToTwoBit /storage/reference/11.GRCm39/Mus_musculus.GRCm39.dna.toplevel.fa Mus_musculus.GRCm39.dna.toplevel.2bit
twoBitInfo Mus_musculus.GRCm39.dna.toplevel.2bit stdout | sort -k2,2nr > Mus_musculus.GRCm39.dna.toplevel.chrom.sizes
/storage/reference/13.cross.species/01.create.chain/parasol/nodeInfo/nodeReport.sh 0 /storage/reference/13.cross.species/01.create.chain/parasol
/storage/reference/13.cross.species/01.create.chain/parasol/initParasol start
time (/storage/reference/13.cross.species/01.create.chain/scripts/doBlastzChainNet.pl ./DEF -verbose=2 -noDbNameCheck \
    -workhorse=localhost -bigClusterHub=localhost -skipDownload \
    -dbHost=localhost -smallClusterHub=localhost -trackHub \
    -fileServer=localhost -syntenicNet)
/storage/reference/13.cross.species/01.create.chain/parasol/initParasol stop
I then used the qsub to submit it to the computing node, where it ran for a few days and generated the "psl" and "run.blastz" directories in the target directory, but the task just kept updating the "batch" file in the "run.blastz" directory and didn't generate anything new in the "psl" directory, I don't know if that's right. I feeling upset because your team already provided detailed BLASTZ parameters and I have not been able to create a chain file, any suggestions would be very helpful.

Best regards,
Fuwen


汪富文(Fuwen Wang)
Ph.D Candidate
College of Animal Science and Technology, Northwest A & F University
Yangling, Shaanxi 712100, China

Hiram Clawson

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Aug 12, 2024, 10:27:54 PM8/12/24
to 汪富文, genome
Good Evening Fuwen:

Please note the chain tracks on the goat assembly:

https://genome.ucsc.edu/h/GCF_001704415.2

this assembly is identical to GCA_001704415.1
with some contamination removed.

I will start the process to get the mouse and pig lift over
alignments.

--Hiram

Luis Nassar

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Aug 14, 2024, 7:19:45 PM8/14/24
to Hiram Clawson, 汪富文, genome

Hello, Fuwen.

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. We have gone ahead and generated those liftOver files for you:

https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCF_001704415.1.over.chain.gz
https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/liftOver/susScr11ToGCF_001704415.2.over.chain.gz
https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToSusScr11.over.chain.gz
https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.1/liftOver/GCF_001704415.1ToMm39.over.chain.gz

Let us know if you require any additional assistance, or would like to troubleshoot the blastZ pipeline.

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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汪富文

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Aug 15, 2024, 12:11:00 PM8/15/24
to Luis Nassar, Hiram Clawson, genome
Hi,
I sincerely appreciate your help to me. If I have time, I will continue to explore how to build chain using UCSC pipeline. I have read a lot of forum discussions and admire your patience and professionalism very much. I hope your team gets better and better！！


汪富文(Fuwen Wang)
Ph.D Candidate
College of Animal Science and Technology, Northwest A & F University
Yangling, Shaanxi 712100, China



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