Question: Fastq Trimmer problem
0
gravatar for andrew.j.skelton73
4.4 years ago by
London
andrew.j.skelton735.5k wrote:

I have a set of fastq files and I want to trim from the adaptor sequence to the 3' end, are there any trimmers that can do this?

Example:

5' -> AAATTAACGGGG ATCGATCGATCG TTGGGGTGGGTG <- 3'

Adaptor Sequence -> ATCGATCGATCG

What I want extracted -> AAATTAACGGGG

fastq rna-seq • 1.1k views
ADD COMMENTlink modified 4.4 years ago by Dan D6.7k • written 4.4 years ago by andrew.j.skelton735.5k
1

yes that's the most common situation in which you have to trim adapter sequences. see for example Trimmomatic or cutadapt. I guess you could have found such tools by searching biostars

ADD REPLYlink written 4.4 years ago by Martombo2.4k

if I remember correctly, you could set what part od read you want and which you want to discard with -a and -g options

ADD REPLYlink written 4.4 years ago by Biomonika (Noolean)3.0k
2
gravatar for Dan D
4.4 years ago by
Dan D6.7k
Tennessee
Dan D6.7k wrote:

As Martombo indicated, cutadapt can do this. You will need to use the -a option. So your command would look like this:

cutadapt -a ATCGATCGATCG -o [output FASTQ file] [input FASTQ file]

By default, it will trim any adapter that matches at least 3 bases of your sequence. I think this is too stringent, and I usually change this behavior using the -O parameter.

ADD COMMENTlink written 4.4 years ago by Dan D6.7k
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