commandlines and sequences
Which command can I use to grab the first 10 nucleotides in each line of my nucleotide sequence in a file?
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GenoMax
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Baby Bioinformatician
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Baby Bioinformatician
1 answer
You can use reformat.sh from BBMap suite to do this.
reformat.sh in=infile.fq out=outfile.fq ftr=9
If you have paired-end data then you would want to use something like this
reformat.sh in1=infile_R1.fq in2=infile_R2.fq out1=outfile_R1.fq out2=outfile_R2.fq ftr=9
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What have you tried? Otherwise this is a pure programming question.
I'd suggest starting with the biopython cookbook and tutorial. The solution to your problem is in there.
Refer to tips and tricks on trimming ngs data online.
Use google please!