[maq-help] consensus fastq to fasta?

[Gibbons, J. G. <john.g.gibbons@Vanderbilt.Edu>]

Hello,
I have been using Maq for the last couple years and have been using a very roundabout way to get at some information that I routinely use.

I typically work with Illumina population data. For phylogenomic purposes, I map my reads, call SNPs in all samples then pull out all of the variant sites from the consensus fasta file, which I generate from the consensus fastq file (with the 'cns2fq' command).

I am not a programmer so I used a variety of sed and grep commands to produce a fasta file from the fastq file.

My question is has anyone created a script to generate a fasta file from the consensus fastq file? I would be incredibly grateful for a script that could accomplish that.

Thanks,

John

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John G Gibbons
Department of Biological Sciences
VU Station B, Box 35-1634
Vanderbilt University
Nashville TN, 37212
The Rokas Lab
Email: John.G.Gibbons@Vanderbilt.Edu<mailto:John.G.Gibbons@Vanderbilt.Edu>
Tel: (615) 936-3893
http://sitemason.vanderbilt.edu/people/jggibbons