It is actually unzipped and it gave me 6-lines when running your line
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Getting sequences from fastq file using Grep command
I have been trying to get a sequence (e.g. GCGAGCCCCACATCGCCCCCCCGATTGTAATAAATAA) from a fastq file (file.fastq) I have and output a fq file. I have tried the command:
grep -A 2 -B 1 'GCGAGCCCCACATCGCCCCCCCGATTGTAATAAATAA' file.fastq | sed '/--/d' > output.fq
I got an output as 6- lines of reads that are different, while my target sequence is basically more in number. A part from that they might be just not there, Are the - A and - B is getting only the upstream and trailing sequences surroundng my target or do they get these along with the target sequences. I red the -- help page, but could not understand it. Thanks for any help.
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mohsamir2016 •
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3 answers
Use bbduk.sh from BBMap suite in filter mode. grep has its place but a proper tool is foolproof.
bbduk.sh -Xmx2g in=your.fq outm=filtered.fq literal=GCGAGCCCCACATCGCCCCCCCGATTGTAATAAATAA
Add rcomp=f if you don't want to find reverse complemented sequence.
Try seqkit grep, which searches on both strands, you might need to add --only-positive-strand.
seqkit grep -s -p GCGAGCCCCACATCGCCCCCCCGATTGTAATAAATAA file.fastq -o out.fq.gz
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use
--no-group-separatorinstead of sedAre you confident this sequence will only appear once?
Actually it is much longer I only gives example...
let's try another way. Show us the output of:
Could you let me know what paste is doing ?
Thanks
Converting to a single line