Split a fq file into two fq files by length.
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11 days ago

There is an fq file after trimming. I want to split it into two fq files, one for the first 1-34 nt and the other for 35-71 not, but I don't know what command to write. I would appreciate it if you could help me.

split fastq • 247 views
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11 days ago
seqkit subseq -r 1:34 in.fq.gz -o a.fq.gz

seqkit subseq -r 35:-1 in.fa.gz -o b.fq.gz

But if it's amplicon sequencing, it would not so easy. seqkit amplicon may help.

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11 days ago
gunzip -c in.R1.fq.gz  |\
paste - - - - |\
awk -F '\t' '{L=length($2);F="";if(L<=34) {F="f34.fq"} else if (L<=71) {F="f71.fq"} else {next;} printf("%s\n%s\n%s\n%s\n",$1,$2,$3,$4) >>F;}'
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11 days ago
GenoMax 115k

You could also use reformat.sh from BBMap suite.

# to get the left part of the read

reformat.sh -Xmx2g in=input.fq.gz outm=out.fq.gz forcetrimright=34

# to get the right part of the read

reformat.sh -Xmx2g in=input.fq.gz outm=out.fq.gz forcetrimleft=34
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11 days ago

for bases from 1-34:

cutadapt -u -37 <input.fastq> -o <output.fastq>

for bases from 35th onwards including 35th base

cuatadapt -u 34 <input.fastq> -o <output.fastq>
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