Fastq Trimmer problem
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
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1 answer
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.
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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
if I remember correctly, you could set what part od read you want and which you want to discard with
-aand-goptions