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Old 05-22-2017, 03:45 PM   #4
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 610

The kind of adapter contamination you want to get rid off is the read-through kind, where you get a piece of fragment that then continues to read into the adapter. These are all taken care of by Trim Galore.

What you sometimes see flagging up as overrepresented sequence is probably something like adapter dimers or concatamers. These are contaminants that, but since they are purely adapter sequence they won't align to the genome anyway and are hence taken care of in the subsequent alignment step. If you look at the sequence of those contaminants you will probably notice that they don't look like the sequence I linked in the thread above, often they are simply lacking the A at the start (from the A-tailing process). In other words, I would recommend you run the adapter trimming as outlined already, and don't bother about additional contaminants as they won't align anyways.

All the best, Felix
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