Friday, 8 October 2010

small RNA analysis for SOLiD data

SOLiD™ System Small RNA Analysis Pipeline Tool (RNA2MAP) is being released as "unsupported software" by Applied Biosystems.

It failed for me at just simply producing the silly PBS scripts to run the analysis. I was advised to run it in another linux server to try by dumb luck :(
I found example scripts but documentation is brief. Not sure if it's worth the hassle to debug the collection of perl scripts or to manually edit the params in the PBS submission scripts for a tool that is not commonly used.

How are you analysing your small RNA SOlid reads? any software to recommend? is for 454 and Illumina
Partek Genomics Suite is commercial

the other two at listed at seqanswers wiki
doesn't seem to be for solid as well.


  1. You're not the only one who has had issues with creating the PBS script.
    It seems first you have to:
    export CORONAROOT=path to RNA2MAP
    export PERL5LIB = path to RNA2MAP/lib/perl

  2. Darn.. is that the issue? sounds like a simple fix!

  3. Worked for me :)
    Now I'm dealing with new bugs...

  4. Oh haha hmmm ok, I tried troubleshooting for a day then I gave up. I managed to print the final command instead of just the help logs. Can't remembered if that worked out completely. It might be complicated for me as I have BIOSCOPEROOT installed as well.
    Good Luck!


Datanami, Woe be me