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Old 02-28-2011, 10:03 PM   #5
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Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

If you are analyzing RNAseq data why are you using bowtie and not tophat? Your percent aligned will be low with bowtie alone as only reads aligning to an exons will map, while all reads crossing a exon-exon junction will not align. Depending on the read length this can be a large percentage or your reads.
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