Question: cutadapt --cut option for paired-end reads?
0
gravatar for blur
2.3 years ago by
blur90
European Union
blur90 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 • 993 views
ADD COMMENTlink modified 2.3 years ago by Marcel M70 • written 2.3 years ago by blur90
1

Did you read the manual?

ADD REPLYlink written 2.3 years ago by WouterDeCoster37k

actually he is repeating the question with different title :)

C: uneven paired end reads in bowtie

ADD REPLYlink written 2.3 years ago by Medhat8.2k
1
gravatar for Marcel M
2.3 years ago by
Marcel M70
European Union
Marcel M70 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 2.3 years ago by Marcel M70
0
gravatar for b.nota
2.3 years ago by
b.nota6.4k
Netherlands
b.nota6.4k wrote:

I would advice to use Trim Galore instead.

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

ADD COMMENTlink written 2.3 years ago by b.nota6.4k
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