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Old 11-26-2018, 07:04 AM   #1
lre1234
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Default Separating human and mouse sequence reads from RNA-seq data

HI all,
A collaborator is doing an experiment in which their will be a human xenograph into a mouse model, followed by RNA-seq. Most likely there will be a mixture of human and mouse transcripts in there. Has anyone done something to deal with this? Is there a way to dissociate the two sets of transcriptomes?
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Old 11-26-2018, 08:00 AM   #2
GenoMax
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Take a look at bbsplit from BBMap suite.

There are other tools like XenofilteR for this application as well.
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Old 11-26-2018, 04:47 PM   #3
cmbetts
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The way I handled it in the past was to build my STAR index with both genomes/annotations simultaneously making sure to rename the chromosomes such that they're unique ("human_chr1" and "mouse_chr1" instead of both "chr1"). That way the aligner puts the reads on the correct genome and reads with too much species conservation end up as multi-mapped and not counted.
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