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  • question about mapping reads back to an endosymbiont genome

    Hi All,

    I'm new to the forum and to RNA-seq, and the sequencing project I'm working on is a bit tricky. The experiment I'm doing is basically a single Illumina HiSeq run, just to see if and how many reads we can detect from the bacterial endosymbiont we're interested in from a total RNA sample. We have a draft genome, but it's not complete. It's basically a fasta file of assembled contigs plus short reads.

    So, I was thinking to align my data using bowtie and assemble transcripts with cufflinks. I've searched the literature a little bit but couldn't find a source that gave details about how to map metatranscriptome data back to a single reference genome from a symbiont. Does anyone have advice about how to reduce the likelihood that an aligned read is from a homolog from a related bacteria?? I will set the mismatch allowances in bowtie to 0, but other than that I'm a little stuck as to what else to do for quality control. Thanks for the help!!

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