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coverage of the customized genome #58
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Hi Wei, |
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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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
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