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Old 02-28-2010, 04:29 PM   #1
hrajasim
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Default miRNA-seq - mapping to MIRBASE

Hi Folks,

I am am trying to analyze the first set of miRNA reads. We did a 36 base single reads with adaptors of size upto 14 bases. I aligned the 22 bases against the reference genome. This went OK - but makes little sense for miRNAs.

Now, I am running into several issues w.r.t. aligning the 22 base reads against the miRBase. But I hear that this is being done routinely for miRNAs.
I have the miRBase .fa files squashed and created the genome_size.xml file using the squashGenome command. However, when I try to run the cmd runRNA, I get the message "not a recognized reference genome..."

Could someone point me to detailed instructions on how to map, count, classify miRNA as known miRNA, non-coding, etc?

Has anyone tried miRTools http://centre.bioinformatics.zj.cn/mirtools/ ? culd you share your experiences, tips, tricks?

Thanks,
Harsha
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