5.3 years ago by
I have done some similar work with my small RNA sequences. I used proTRAC software to identify any piRNA clusters. proTRAC is developed by Dr.David Rosenkranz's group. THis can be run on command line or as a user interface. I have used command line options The pdf for the user documentation mentions , to use a probabilistic option if the samples are not selectively enriched for piRNA sequences (martombo's suggestion here might help !) and has contamination with other tRNAs etc.
My samples were generated to exclusively enriching for miRNAs but also see fragments of tRNAs etc as the source is from exosome ! However I just ran the default parameters and still obtained clusters. Although my analysis is not complete I was excited to introduce this software on this forum as proTRAC uses the information on IBAB, and other traditional piRNA sources and has shown to work better in predicting clusters that IBAB missed. Something worth checking out : http://sourceforge.net/projects/protrac/
I would appreciate any inputs on the use of proTRAC if anyone has had the opportunity to use it !