How to parse FASTQ file?

Shishir · 02-01-2013, 04:37 AM

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?

GenoMax · 02-01-2013, 05:03 AM

Have you considered using "awk"?

Shishir · 02-01-2013, 05:34 AM

Thanks!
I searched for "awk" and realize "sed" can do it easily

kopi-o · 02-01-2013, 05:42 AM

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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02-01-2013, 04:37 AM	#1
Shishir Member Location: Germany Join Date: Nov 2012 Posts: 22	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?

02-01-2013, 05:03 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Have you considered using "awk"?

02-01-2013, 05:34 AM	#3
Shishir Member Location: Germany Join Date: Nov 2012 Posts: 22	Thanks! I searched for "awk" and realize "sed" can do it easily

02-01-2013, 05:42 AM	#4
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	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 :-)