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Old 12-15-2016, 07:36 PM   #103
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

If you know your adapter sequences (or have a list of typical adapter sequences, or actually, you can just say "adapter=default"), you can do this:

Code: in=reads.fq adapter=adapter.fa out=merged.fq outu=unmerged.fq
If BBMerge thinks that you still have untrimmed adapters in those cases... I am quite confident it is correct. Adapter-trimming programs are not perfect (nor is BBMerge or BBDuk). I recommend BBDuk for adapter-trimming because it uses both adapter sequences and overlap information (very conservatively), but you will still end up with some untrimmed reads that actually had adapters. The problem is that Illumina sequence quality declines with each cycle, so by the end of the read (the part that typically overlaps, or has adapter sequence) the error rate can be pretty high. If you use an adapter-trimming program that solely uses sequence-matching to a list of provided adapter sequences, then the high mismatch rate will yield poor adapter-trimming for low-quality reads. BBDuk with the "tbo" flag uses both adapter sequences and overlap information, which for short-insert reads, gives added weight to the high-quality initial bases in a read pair.

So - it's not surprising that Trimmomatic did not do complete trimming. I recommend you use BBDuk instead. It still won't give perfect adapter-trimming, but it will be much better than Trimmomatic.
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