[mira_talk] Re: Fastaq to fasta and qual
- From: "Shai Uliel" <shai@xxxxxxxxxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 24 Sep 2009 14:15:11 +0200
If you have short reads (1 line seq) you can write: grep -A1 '^@'
in.fastq | grep -v '^-' | sed 's/^@/>/' > out.fasta
And
grep -A1 '^+' in.fastq | grep -v '^-' | sed 's/^+/>/' >
out.fastq
From: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Torsten Thomas
Sent: Thursday, September 24, 2009 4:22 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Fastaq to fasta and qual
Hi.
Does anybody have a script that converts a fastaq file to a
corresponding fasta and fasta.qual file?
And if yes, are you willing to share it. :-)
Cheers
Torsten
Dr. Torsten Thomas
Senior Research Fellow
Centre for Marine Bio-Innovation
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney, NSW 2052
Australia
Ph + 61 (0) 2 938 53467
Mob +61 (0) 410159525
Fax + 61 (0) 2 938 51779
"Anyone who believes exponential growth can go on forever in a finite
world is either a madman or an economist" (Kenneth Boulding, economist)
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