Question: Fasta Generation From Pileup For Snp Detection
gravatar for John David Osborne
7.8 years ago by
John David Osborne160 wrote:
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. -John
alignment bowtie samtools bam • 1.3k views
ADD COMMENTlink written 7.8 years ago by John David Osborne160
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour