NGS users

[archana]

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

[dpryan]

That's an annoying format that you have to deal with. You can split each line and output things in fastq format with:

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.

[Brian Bushnell]

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

[archana]

Thankyou sir.. it worked well.