cutadapt --cut option for paired-end reads?

Question

[blur]

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...

[WouterDeCoster]

Did you read the manual?

[Medhat]

actually he is repeating the question with different title :)

C: uneven paired end reads in bowtie

Answer 1

[Marcel M]

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.

Answer 2

[Benn]

I would advice to use Trim Galore instead.

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