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I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the two, therefore I wonder what is the best tool to do this? I have single-end reads. What I need is to have a percentage of uniquely mapped fragments, mapped to multiple loci and, say, unmapped. Can bowtie do the job? Is there a standard explanation procedure explained elsewhere? Thanks.

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This is a pretty straightforward analysis, assuming that you want to measure something like "how many reads align to genome 1, and how many reads align to genome 2?".

You should be able to then use samtools to compute statistics on your alignments.

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