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Old 03-15-2014, 06:18 PM   #3
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I can't help you with Cutadapt, but if you want to use BBDuk, the command is: in1=read1.fq in2=read2.fq out1=trimmed1.fq out2=trimmed2.fq ref=adapters.fa ktrim=r k=25 mink=12 hdist=1

That will trim adapters toward the 3' end, starting with the first instance of any 25-mer in the reference. If there are no 25-mer matches, it will try to match as few as 12bp from the adapter end to the read 3' end. 'hdist=1' allows a hamming distance of 1 (1 mismatch). 'adapters.fa' should be a valid fasta file with all the adapters (so the name of each adapter needs a '>' symbol).

If you only have single-ended reads, you can omit in2 and out2. But with paired reads it's best to trim both reads at the same time or else they may lose sync (if some reads are discarded because they are entirely adapter). And at least for our lab, both reads get the same TruSeq adapters on the 3' end in a normal library.
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