Question: cutadapt --cut option for paired-end reads?
0
gravatar for blur
3.0 years ago by
blur110
European Union
blur110 wrote:

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 • 1.3k views
ADD COMMENTlink modified 3.0 years ago by Marcel M90 • written 3.0 years ago by blur110
1

Did you read the manual?

ADD REPLYlink written 3.0 years ago by WouterDeCoster42k

actually he is repeating the question with different title :)

C: uneven paired end reads in bowtie

ADD REPLYlink written 3.0 years ago by Medhat8.6k
1
gravatar for Marcel M
3.0 years ago by
Marcel M90
European Union
Marcel M90 wrote:
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.

ADD COMMENTlink written 3.0 years ago by Marcel M90
0
gravatar for Benn
3.0 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

I would advice to use Trim Galore instead.

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

ADD COMMENTlink written 3.0 years ago by Benn7.9k
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