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Old 02-01-2013, 03:37 AM   #1
Shishir
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Default How to parse FASTQ file?

I am new in NGS. I need to format some fastq files. For example I want to replace characters /1 and /2 with -1 and - 2 in the files having data like @HWUSI-EAS1671_0001:5:1:1022:10290/1.
I tried to do it in perl with pattern matching but the files are too big to parse. Could anyone please give me suggestion on share any code?
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Old 02-01-2013, 04:03 AM   #2
GenoMax
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Have you considered using "awk"?
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Old 02-01-2013, 04:34 AM   #3
Shishir
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Thanks!
I searched for "awk" and realize "sed" can do it easily
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Old 02-01-2013, 04:42 AM   #4
kopi-o
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The files are surely not too big to parse with perl (for your purposes) if you do it right - you only need to have four lines at a time (or maybe just one) in memory. Also it might be a good opportunity to learn some BioPerl :-)
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bioinfomatics, fastq, next gen sequencing, rna seq

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