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Old 11-28-2014, 06:07 AM   #2
blancha
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Location: Montreal

Join Date: May 2013
Posts: 367
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As far as I know, you can only trim one adapter at a time with fastqx_clipper or cutadapt.
You'll have to trim them one after the other if you have different adapters for the reads.

Note that, with Cutadapt at least, you only need to trim the first adapter after the insert.
This sequence is generally identical for all the reads. It doesn't matter if the sequences differ after the first adapter.

With Trimmomatic, you can give in argument an adapter file with all the adapter sequences.
http://www.usadellab.org/cms/?page=trimmomatic
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