Filtering fastq file
I have a fastq files and I found many reads with only N. I want to filter only those reads which contains N. Any one liner for that?
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Brian Bushnell
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To separate reads with Ns using BBMap:
bbduk.sh in=reads.fq out=readsWithoutNs.fq outm=readsWithNs.fq maxns=0
If you have, say, 100bp reads and only want to separate reads containing all 100 Ns, change that to "maxns=99".
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gunzip -c input.fastq.gz | paste - - - - | awk -F '\t' '!($2 ~ /N/)' | tr "\t" "\n" > noN.fq
remove the '!' to get the 'N' only
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Pierre Lindenbaum
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You can use
bbduk.shorreformat.shfrom BBMap suite withqtrim=rl trimq=1. That will only trim trailing and leading bases with Q-score below 1, which means Q0, which means N (in either fasta or fastq format). If the entire read is N then it will be taken out.It didnt work they way you said. I want all the reads with N in separate file.
Use
outm=to grab filtered reads is a separate file. If you have a paired-end data set then you can useoutm1=andoutm2=to grab both reads.bbduk.sh in=file.fq qtrim=rl trimq=1 out=clean.fq outm=capture.fq minlength=read_length. This will capture any read that has at least one N in theoutmfile (replace read_length = number of cycles in your reads).Note: This will trim the N's out though. Which is not what you seem to want. So use @Pierre's solution for now until I (or Brian Bushnell ) can help figure out a BBMap way.
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