Co-culture data to align to multiple genomes

[C9r1y]

Hello,

I am looking for a way to align Illumina data to two different bacterial genomes. I have been using bowtie, and thought at first to keep the genomes separate, but I also have created a merged fasta file. Once aligned, any idea of good analysis pipeline? This data is of 8 samples, some of which are from co-cultures of the two bacteria types. Thanks for any ideas.

[swbarnes2]

Hello,

I am looking for a way to align Illumina data to two different bacterial genomes. I have been using bowtie, and thought at first to keep the genomes separate, but I also have created a merged fasta file. Once aligned, any idea of good analysis pipeline? This data is of 8 samples, some of which are from co-cultures of the two bacteria types. Thanks for any ideas.

For sure, align to a reference multi-fasta that has both possible genomes. The last thing you want is for the software to take a read that matches genome 1, and be forced to align it to genome 2, because you didn't give it the option of aligning to genome 1.

After aligning, you can use samtools or awk or whatever to break down the .bam, and look at which reads align where, and how uniquely.