Fastq Trimmer problem

Question

[andrew.j.skelton73]

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

[Martombo]

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

[Biomonika (Noolean)]

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

Answer 1

[Dan D]

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.