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cutadapt --cut option for paired-end reads?

Hi, I have paired-end read data, and I need to remove 10 bp at the end of R1 ans the first 10bp in R2 - how can I do this without ruining the pairs? I tried cutting each read on its own, and ended up with unmatched sized reads that I couldn't align in bowtie...

cutadapt
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updated by Marcel M Marcel M • written by blur blur

2 answers 

cutadapt -u 10 -U -10 -o out.1.fastq.gz -p out.2.fastq.gz in.1.fastq.gz in.2.fastq.gz

The -u 10 removes 10 bp from the 5' end of read 1; the -U -10 removes 10 bp from the 3' end of read 2.

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written by Marcel M Marcel M

I would advice to use Trim Galore instead.

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

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written by Benn Benn

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