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Old 08-31-2015, 06:02 AM   #1
Location: New York

Join Date: Nov 2012
Posts: 49
Question How can I identify homologous genes between these two datasets?

Hi. Thanks for taking the time to read my question. I am a PhD student and need some help getting over a bump on a project I'm working on.

I have a RNA-seq dataset. I aligned the reads to the reference genome with bowtie2, I have a bam file for this.

I assembled a genome from the same reads using Trinity, then aligned the reads to the assembly using bowtie2. I have a bam file for this. I have also ordered contigs based on the reference genome using Mauve, and did some genefinding using RAST. It's not a perfect assembly by any means.

I want to check gene expression levels between these two cases, but that means I have to identify the homologous genes. I need to be able to say, "In the first case gene A is expressed this much, and in the second case gene A is expressed that much." I just am not sure how to get there from where I'm at now. I was thinking maybe I somehow have to blast the data and parse out position values or something, but I'm not sure. I feel like people must have seen this problem before.

I really appreciate any advice anyone can offer. Thanks very much in advance!
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