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.
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.
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