Question: cn.mops on CRAM files
0
gravatar for dsilencio
5 months ago by
dsilencio0
dsilencio0 wrote:

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 • 109 views
ADD COMMENTlink modified 5 months ago by Günter Klambauer540 • written 5 months ago by dsilencio0
Answer: cn.mops on CRAM files
0
gravatar for Günter Klambauer
5 months ago by
Austria
Günter Klambauer540 wrote:

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 COMMENTlink written 5 months ago by Günter Klambauer540
1

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

ADD REPLYlink written 5 months ago by Martin Morgan ♦♦ 24k

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 REPLYlink written 5 months ago by dsilencio0

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 REPLYlink written 5 months ago by Günter Klambauer540
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