Question: Using BWA with Illumina data and metagenomic "reference genome"
0
gravatar for agent.diamond
3.4 years ago by
Canada
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?

Thanks

Liz

bwa • 1.3k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson24k • written 3.4 years ago by agent.diamond0
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Fasta is the correct format for a Custom Reference genome. More details are here:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Differential expression analysis can be performed on the public Main Galaxy instance at http://usegalaxy.org with the Tuxedo suite, under the tool group "NGS: RNA-seq". Tutorials and other help are here:
http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson24k
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