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r3fang / SnapTools

A module for working with snap files in Python
Apache License 2.0
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Question about adding Genomes in snaptools snap-pre #11

Closed Austin-s-h closed 5 years ago

Austin-s-h commented 5 years ago

Hi! Thanks for building this package, it's been really helpful so far! I had a question about using snap-pre. I work in chicken, and we recently had a new assembly come out (galGal6) that I've aligned my reads to. (and generated appropriate chrom.sizes) When I specify --genome-name galGal6 it throws an error asking me if the name is correct. Since it works with --genome-name galGal5 I've just used that and run, but will this cause issues down the line?

Thanks! Austin

r3fang commented 5 years ago

Hi Austin,

It will not cause any issue for downstream analysis.

Best,

Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On May 23, 2019, at 4:55 PM, Austin-s-h notifications@github.com wrote:

Hi! Thanks for building this package, it's been really helpful so far! I had a question about using snap-pre. I work in chicken, and we recently had a new assembly come out (galGal6) that I've aligned my reads to. When I specify --genome-name galGal6 it throws an error asking me if the name is correct. Since it works with --genome-name galGal5 I've just used that and run, but will this cause issues down the line?

Thanks! Austin

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wangmhan commented 4 years ago

Hi Austin, It will not cause any issue for downstream analysis. Best, -- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego … On May 23, 2019, at 4:55 PM, Austin-s-h @.***> wrote: Hi! Thanks for building this package, it's been really helpful so far! I had a question about using snap-pre. I work in chicken, and we recently had a new assembly come out (galGal6) that I've aligned my reads to. When I specify --genome-name galGal6 it throws an error asking me if the name is correct. Since it works with --genome-name galGal5 I've just used that and run, but will this cause issues down the line? Thanks! Austin — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11?email_source=notifications&email_token=ABT6GG6A3PX4IPNOA244A3DPW4AD7A5CNFSM4HPKGVK2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GVR6ERA>, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG7VCM22RPM5GZKY6GDPW4AD7ANCNFSM4HPKGVKQ.

Hi, I also have a similar question. It seems snaptools snap-pre cannot recognize homemade name. To my understand, for example here, when we created index via snaptools index-genome, the --output-prefix should be galGal5 though the actual fasta is galGal6. Then, the next step via snaptools snap-pre, still use galGal5. Is it correct? Or it will use internal real galGal5 to create snap files?

Thanks & best, Menghan