small RNA Tool for SOLiD reads failed any alternatives?

[KevinLam]

Hi
SOLiD™ System Small RNA Analysis Pipeline Tool (RNA2MAP) is being released as "unsupported software" by Applied Biosystems.
see http://solidsoftwaretools.com/gf/project/rna2map/

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?
http://seqanswers.com/wiki/MirTools is for 454 and Illumina
Partek Genomics Suite is commercial

the other two at http://seqanswers.com/wiki/Special:B..._transcriptome
doesn't seem to be for solid as well.

[tandonm]

I'm coming across this problem too! It has been described before in the forums for that tool (http://solidsoftwaretools.com/gf/pro...e&forum_id=230), but it seems it has not been resolved. I did some work trying to track down the cause of the error and you can read about that at the aforementioned forum by following the link, but I am still at a loss, and our data continues to go unanalyzed!

Please do let me know if anyone was able to come up with a work-around for this issue, or if you have any leads at all. Thanks!

[KevinLam]

I didn't manage to get far as well.
I recall that I might have extracted out the commands for the script. but it failed along the way as well.

Some recommended using Novoalign to align the solid reads.
I believe I saw a post in seqanswers to use bioscope to map the reads instead. and work downstream with other tools.

Have you tried asking ABI support? Did they give any helpful answer?

[tandonm]

I was thinking about using bioscope directly, because I think the small RNA pipeline is just an implementation of that package. I'll look at Novoalign as well.

ABI specifically says that the pipeline is "unsupported software," so I'm not sure how to get in touch with the programmers to get help finding the issue. I posted on the associated forum though, which may be the best way to get their attention.

Thanks for the input!

[tandonm]

I think I found a solution to this problem. In fact, it was basically solved in the last few posts of the first forum thread (here), with the suggestion that the CORONAROOT variable needs to be exported. It was a little ambiguous though, and being a newbie, I did not understand the implications when I first read it. So, I have outlined my understanding and solution of this issue on forums here.

As I say in that post, I am not sure if it is a sure fix yet, but I will update this thread as I know more. Thanks!