Mapping rRNA reads

[aganley]

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

[Melissa]

If you have RNA-seq data and map those reads back to yeast ribosomal RNAs reference sequences (28S, 18S & etc), there shouldn't be a problem... provided nothing wrong with the mapping.

[aganley]

Yeah, I've actually been able to get them to map back to the rDNA when its by itself, but not as part of the genome. Which is curious, but this is good enough for my purposes.

Thanks

[Thomas Doktor]

Are you using a repeatmasked reference genome? That might mask out the rRNA genes (depending on what you consider a repeat or not, I believe UCSC stores the rRNA genes in its repeat tracks) and explain why you don't see any mapping to these regions.

[aganley]

Sorry for the late reply. No, our rDNA sequences are in the genome - I can map to them when using genomic DNA reads, but not with transcriptome data. That leads me to think that the program has some issues with an unusually high number of reads mapping to a short region, and hence doesn't map them. It (mostly) works when I use a single rDNA unit as the reference genome, but even sometimes then it doesn't work (for reasons I don't understand).