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Old 08-10-2016, 11:26 AM   #4
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Location: Bioo Scientific, Austin, TX, USA

Join Date: Jun 2012
Posts: 119

I think this is what you need:

cutadapt -a AGATCGGAAGAG -o YOUR_FILE.trim1.fq --minimum-length 15 YOUR_FILE.fastq.gz

You don't need to put in the index sequence, as cutadapt will remove anything 3' of the adapter sequence, unless you specify otherwise. The minimum length command will throw out any reads less than the specified value. I think the default allowed error rate is 0.1, which should be fine.

It does look like you can use the --trim-n option to remove the first N.

It probably isn't necessary to quality trim, although you may want to quality filter before the adapter trimming. Also probably no need for the -g command, unless this was a particular kind of library where you expect to see adapter sequence at the 5' end of the read.
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