Small Rna Analysis

Question

[Janake]

I am analyzing a small RNA data set that we generate from Illumina GAII. This organism doesn't have a sequenced genome. How can I get rid of rRNA, tRNA, snRNA, and snoRNA, as well as those containing the polyA tail?

Answer 1

[Prateek]

This may be a starting point..

1. You can use tRNA-scan-SE to mask out tRNA http://lowelab.ucsc.edu/tRNAscan-SE/

2. Mask out other ncRNA (5S, 16S, 18S, and 23S rRNA) using blast - you may easily find multi-fasta files of these from somewhere.

3. check this out http://www.ncrna.org/frnadb/download - you can use there ncRNA fasta file to blast against.