Question: How to take reads from WGS fastq files in order to map it with Exome?
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gravatar for jonessara770
13 months ago by
jonessara770170
jonessara770170 wrote:

Hi

I have a fastq files from WGS but I want to subsample the reads and just runs it as WES, is there a way to do that?

Thanks Sara

wgs • 340 views
ADD COMMENTlink written 13 months ago by jonessara770170

Why not map as usual and find out which reads map to the exome?

ADD REPLYlink modified 13 months ago • written 13 months ago by genomax74k

Actually, because my pipeline is not optimized for WGS and it takes a lot of time to run the WGS so I want just subsample and map it to WES?

ADD REPLYlink written 13 months ago by jonessara770170

You don't know which reads come from exonic regions until you map them. As far as I know your only option would be to first map them all and then, if needed, extract the "exome" regions.

ADD REPLYlink written 13 months ago by bernatgel2.2k
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