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Old 04-02-2013, 01:57 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

For starters, don't worry about quality filtering your reads.

Software like bwa and bowtie are designed to take two separate fastqs for paired end data. If you cat them together, that's like submitting a single end file. Which is fine, but you lose the benefit of paired end reads. As long as the order of the reads in the two separate files is undisturbed, bwa and bowtie will understand that they are paired.

You can get rid of exact duplicate pairs with samtools rmdup, or Picard's MarkDuplicates.

samtools idxstats will tell you how many reads there are per sequence in your reference.
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