Which command can I use to grab the first 10 nucleotides in each line of my nucleotide sequence in a file?
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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version 2.3.6
Use google please!
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.