search

brentp / goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
MIT License
212 stars 24 forks source link

coverage of the customized genome #58

Open weizhu365 opened 5 years ago

weizhu365 commented 5 years ago

Dear Brent;

I build a customized genome sequence by adding a new sequence "VectorA" (~ 10kb) to hg19, and I would like to have coverage of the VectorA via your tool indexcov. I have tried different combination of the command arguments, including --includegl and -c. However, none of them to have the VectorA depth either in the plot or in the file indexcov-indexcov.bed.gz. The vector is less than 16k, so it is reasonable there is no plot. But could you tell me how to have the result in *-indexcov.bed.gz file?

Thanks,

Wei

brentp commented 5 years ago

Hi Wei, indexcov doesn't report any values if the length of the chromosome is < 16KB. For such a small chromosome, I think you'd do better using mosdepth which will calculate the depth quite quickly, especially if you give it just that chromosome. I could probably update indexcov to report estimated, normalized depth for small chromosomes, but it won't be very accurate.

weizhu365 commented 5 years ago

Many thanks for your rapid reply. Best, -Wei

From: Brent Pedersen notifications@github.com Reply-To: brentp/goleft reply@reply.github.com Date: Friday, July 19, 2019 at 10:59 AM To: brentp/goleft goleft@noreply.github.com Cc: Wei Zhu weizhu365@gmail.com, Author author@noreply.github.com Subject: Re: [brentp/goleft] coverage of the customized genome (#58)

Hi Wei, indexcov doesn't report any values if the length of the chromosome is < 16KB. For such a small chromosome, I think you'd do better using mosdepth https://github.com/brentp/mosdepth which will calculate the depth quite quickly, especially if you give it just that chromosome. I could probably update indexcov to report estimated, normalized depth for small chromosomes, but it won't be very accurate.

‹ You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/goleft/issues/58?email_source=notifications&email _token=ABCPMAALU6GW73J6S2AENDLQAHJFTA5CNFSM4IFBBOG2YY3PNVWWK3TUL52HS4DFVREXG 43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2L4HEY#issuecomment-513262483 , or mute the thread https://github.com/notifications/unsubscribe-auth/ABCPMABEYIPKQDLPGRGDQR3QA HJFTANCNFSM4IFBBOGQ . [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/brentp/goleft/issues/58?email_source=notifications\u0026 email_token=ABCPMAALU6GW73J6S2AENDLQAHJFTA5CNFSM4IFBBOG2YY3PNVWWK3TUL52HS4DF VREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2L4HEY#issuecomment-513262483", "url": "https://github.com/brentp/goleft/issues/58?email_source=notifications\u0026 email_token=ABCPMAALU6GW73J6S2AENDLQAHJFTA5CNFSM4IFBBOG2YY3PNVWWK3TUL52HS4DF VREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2L4HEY#issuecomment-513262483", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]