Re: [galaxy-user] Extracting reads mapped from bwa mapping

Hi Austin, As you mention, the difference could be related to how much of the query sequence is actually aligned and passes summary filters. It all depends on the query data, reference genome, and the parameters used for alignment and summary tools. If you do think that a problem exists with

Re: [galaxy-user] Extracting reads mapped from bwa mapping

Just to emphasize the point, the difference between the two methods is an order of magnitude (for a particular example, filtering for flag type gives around 60% of reads mapping, but estimating mapped reads from pileup gave ~5% of reads mapped). Thanks, Austin On Tue, Sep 6, 2011 at 8:40 AM, Aust

[galaxy-user] Extracting reads mapped from bwa mapping

Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to determine the number of reads that were successfully mapped. My question is, I previously thought I could generate a pileup, then sum the number of counts for each base of the reference, and divide this