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Old 11-22-2015, 09:39 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

1) The best practice is to trim the actual adapter sequences used in your library.
2) The best way to find that is to ask the people who made the library.

But, if you have paired reads, you can also find your adapter sequences with BBMerge like this: in1=read1.fq in2=read2.fq outa=adapters.fa

BBDuk includes all standard Illumina adapters in "/resources/adapters.fa". If you do not know which adapters were used, and are unable to find out, I recommend using that as the reference.

Since you are using single-ended reads, it's difficult to automatically empirically determine the adapter sequences. So, unless you can get them from the people who made the library, I suggest using that reference.

Last edited by Brian Bushnell; 11-22-2015 at 09:43 PM.
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