I'm interested in generating a fasta file from Ilumina paired reads of my wild 
type strain. I have an NCBI reference genome I can assemble against and I have 
already uploaded my 2 reads (using the NCBI reference as my genome), used fastq 
groomer, aligned them with bowtie and generated my pileup.

What I think I want to do though is to extract from the pileup a consensus 
fasta file (using 20 or something as a quality cutoff threshold) and then used 
that as my new reference genome to align 2 mutant strains against that are from 
that genetic background. How can I do that in Galaxy? I don't see any way to go 
from pileup to fastaq or pileup to fasta using some sort of cutoff. I think I 
can use samtools pileup2fq based on web posts (and then used something else to 
make a fasta file), but I would like to do all my analysis in galaxy.

Is this possible?

Any help appreciated, I am new with Galaxy.

The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, please use the
Galaxy Development list:


To manage your subscriptions to this and other
Galaxy lists, please use the interface at:


Reply via email to