Question: Using BWA with Illumina data and metagenomic "reference genome"
0
agent.diamond • 0 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
ADD COMMENT
• link
•
modified 4.0 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
4.0 years ago by
agent.diamond • 0
