Take out the read of specific length from fastq files

[figo1019]

hi,
I have fastq files of read length 100 and 94 .Is there a quick shell script to take out the sequences of length 100 from the fastq file.

regards

[seb567]

With biopieces, it is easy.

http://code.google.com/p/biopieces/


cat sequences.fastq | read_fastq | grab -e 'SEQ_LEN >= 100' | write_fastq > sequences_100.fastq

hi,
I have fastq files of read length 100 and 94 .Is there a quick shell script to take out the sequences of length 100 from the fastq file.

regards

[Richard Finney]

cat yourfilename.fq | awk '{if ((NR%4)==0) printf "%s\n",$0; else printf "%s\t",$0;}' | awk '{if (length($2<100) print $0}' | tr "\t" "\n"

Note replace yourfilename.fq with your file name
and edit "<100" according to your needs.