Begin forwarded message:
From: Dan Jones <djones(a)psu.edu>
Date: July 13, 2010 11:02:50 AM EDT
To: Anton Nekrutenko <anton(a)bx.psu.edu>
Subject: galaxy tool suggestion
Hi Anton,
This is Dan (from your bioinformatics class a couple years ago). I have been playing
around on galaxy with a couple of new 454 metagenomics datasets. I have been going back
and forth between the tools 'Build base quality distribution' and 'filter
FASTQ' to assess quality of my data and determine how it is affected by filtering
certain length and quality sequences (using FASTQ lets me simultaneously operate on the
seq and qual scores). I am mainly trying to understand a systematic decrease in quality
that occurs after about 50% sequence length. But, in order to go back and build a base
quality distribution boxplot, I need to extract the qual scores from the fastq file, and I
currently can't find a way to do this on Galaxy (unless I am missing something
obvious, very possible! I see an option to convert fastq to fasta, but I don't get the
.qual file with it). I wrote a short py script to do this (attached), and I think that
something like it to extract a .qual file from FASTQ would be a nice addition to the
galaxy toolbox.
Hope all is well!
Dan
---
Daniel Jones
PhD Candidate, Penn State University
Department of Geosciences
242 Deike Building
University Park, PA 16802
cell: 651-245-2775
lab: 814-865-9340
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org