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Old 04-28-2014, 01:06 AM   #1
archana
Junior Member
 
Location: new delhi, india

Join Date: Apr 2014
Posts: 2
Default NGS users

Hi All,

I am new user to NGS, i got my NGS data in illumina platform, with the format,

HWUSI-EAS481_8291_FC30KTA:3:1:825:1199:GTTAAGTTTATAGATCAGGTGTAGTCGTATGCCGT:hhhhh
hhhhhhhhhhhhhGhhV^hhhhhhhhhhhh
HWUSI-EAS481_8291_FC30KTA:3:1:1027:394:GATGGTCATTATAAAACTTCAATCGTATGCCGTCT:hhhhh
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
can anybody please tell me how to convert it to fastq, input format for pre-processing using FastQ toolkit.

Thankyou,
Archana
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Old 04-28-2014, 02:41 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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That's an annoying format that you have to deal with. You can split each line and output things in fastq format with:

Code:
awk -F ":" '{printf("@%s:%s:%s:%s:%s\n",$1,$2,$3,$4,$5);print $6; print"+"; print $7}' foo.txt > foo.fastq
You'll need to rename "foo.txt" to whatever your files are actually called.
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Old 04-28-2014, 09:06 AM   #3
Brian Bushnell
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Location: Walnut Creek, CA

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That's called "scarf" format. BBTools can translate it to other formats with the "reformat" tool:

reformat.sh in=reads.scarf extin=.scarf out=reads.fq
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Old 05-14-2014, 12:34 AM   #4
archana
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Location: new delhi, india

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Thankyou sir.. it worked well.
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