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brentp / goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
MIT License
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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.

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