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Old 11-26-2015, 03:11 PM   #5
bluepoison
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Location: Detroit

Join Date: Nov 2015
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Thanks a lot for the response Brian.

I have single reads this time. Do you have any suggestions for the overrepresented sequences that do not match with any actual adapter (''No Hit" as described by fastqc)?

Quote:
Originally Posted by Brian Bushnell View Post
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:

bbmerge.sh 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.
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