Hi,
I'm trying to map the rRNA back to a reference genome from an RNA-seq expt using SOLiD data from S.cerevisiae, but nothing maps back to the rDNA (literally nothing).
This is true for ABI's SOLiD software tools as well as Bowtie. I'm pretty sure my polyA purification wasn't 100% (in fact I know there's rRNA in there), so I can't understand why it won't map. ABI don't know, either, so I wondered if anyone else has tried this, or has some idea why it fails?
My best guess is that too many reads are mapping to a small area, and this exceeds some sort of limit in the software (although its curious that ABI and Bowtie software behave the same)....
Thanks
I'm trying to map the rRNA back to a reference genome from an RNA-seq expt using SOLiD data from S.cerevisiae, but nothing maps back to the rDNA (literally nothing).
This is true for ABI's SOLiD software tools as well as Bowtie. I'm pretty sure my polyA purification wasn't 100% (in fact I know there's rRNA in there), so I can't understand why it won't map. ABI don't know, either, so I wondered if anyone else has tried this, or has some idea why it fails?
My best guess is that too many reads are mapping to a small area, and this exceeds some sort of limit in the software (although its curious that ABI and Bowtie software behave the same)....
Thanks
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