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Old 10-11-2012, 05:52 AM   #1
The Snow
Junior Member
 
Location: Italy

Join Date: Jun 2012
Posts: 7
Default Extract aligned reads from a BAM file above a certain threshold

Hello everybody,

I have the following problem: I have a bam file with all the aligned sequences (it was filtered with bamtools filter -isMapped true).

However I would like to filter not only the aligned reads BUT the aligned reads above a certain threshold (e.g. 200) in this way I can filter those sequences that align to a ref with just 1 or two reads

There is a way to do it?

Thanks!

Last edited by The Snow; 10-11-2012 at 07:41 AM.
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