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Old 12-22-2014, 09:02 AM   #3
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

As Brian implied, Trimmomatic will separate the reads into R1_paired, R2_paired, R1_unpaired (e.g., R1 reads that no longer have an R2 mate) and R2_unpaired. Failed reads are thrown away.

I don't use BBDuk -- too lazy to switch from Trimmomatic -- but I think that Brian's example will only produce two files -- one when *both* pairs pass the given parameters (in this case no-phiX, avg quality >= 10) and another file that contains pairs when *either* of the pairs fails. It is also possible to set up BBDuk to output 4 files ala Trimmomatic.

However while the Trimmomatic and BBDuk "pass" files should be effectively the same (given algorithmic differences) the "fail" files will be different with Trimmomatic only having single reads and BBDuk having paired reads.

This is a long winded post that says, yes, use BBDuk if you really want all of the failed reads with all of their warts.
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