Question: Using BWA with Illumina data and metagenomic "reference genome"
gravatar for agent.diamond
4.0 years ago by
agent.diamond0 wrote:

Hi, I'd like to try using BWA to align Illumina reads to some contigs a collaborator made from my Illumina reads (I want to map what reads are in each sample in the assembly of contigs, which I have in FASTA form, or in genes extracted from these contigs with prodigal, also in FASTA form).

What format do I need my contigs/extracted genes to be in in order to use them as a "reference genome", and how can I tell which genes are differentially present in my samples? I assume there is a tool for this?



bwa • 1.6k views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by agent.diamond0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Fasta is the correct format for a Custom Reference genome. More details are here:

Differential expression analysis can be performed on the public Main Galaxy instance at with the Tuxedo suite, under the tool group "NGS: RNA-seq". Tutorials and other help are here:

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
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: 169 users visited in the last hour