Question

cn.mops on CRAM files

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dsilencio • 0

@dsilencio-20971

Last seen 5.5 years ago

Hello,

I have several hundred .cram files that I would like to analyze with cn.mops and would like to avoid converting to a .bam intermediate. Does anyone have experience using .cram as input or using an alternative tool to generate read count matricies from .cram files?

Thanks!

cn.mops • 1.1k views

ADD COMMENT • link updated 5.5 years ago by Günter Klambauer ▴ 540 • written 5.5 years ago by dsilencio • 0

score 0 · Answer 1 · 2019-06-06

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Günter Klambauer ▴ 540

@gunter-klambauer-5426

Last seen 3.8 years ago

Austria

Havent worked with CRAM files, but it should be possible to directly get read counts from them. Will check for solutions.

Maybe anyone from the community could help with this?

Regards, Guenter

ADD COMMENT • link 5.5 years ago Günter Klambauer ▴ 540

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if cn.mops uses Rsamtools, then unfortunately CRAM is not yet supported but this is very much a feature for this release cycle.

ADD REPLY • link 5.5 years ago Martin Morgan 25k

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Thank you all. I will convert to .bam for the time being. Out of curitosity, is it possible to merge the GRanges objects containing count matrices generated from getReadCountsFromBAM? I would like to batch my files, but might be nice to run the cn.mops analysis on a combined dataset.

ADD REPLY • link 5.5 years ago dsilencio • 0

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Yes, you can stack them column-wise (samples) or row-wise (genomic segments). This is exactly what GRanges objects are meant for: easy handling of genomic information data.

ADD REPLY • link 5.5 years ago Günter Klambauer ▴ 540