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Old 07-03-2013, 09:11 AM   #1
angerusso
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Default identifying common reads between mouse and human alignments

Hi,

I have some rnaseq data from xenograft models. I am aligning the reads to human genome and mouse genome separately.

the idea is to throw the reads that are mapped to both human and mouse. How can I achieve this? How can I identify reads that are common to both the human and mouse genome when I run tophat (humanaligned.bam) and mousealigned.bam), then discard these reads and then create a file called "humanminuscommonreads.bam" for the rest of the analysis steps?

Please help.
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