SOCS output

[SOLiD_User]

I am trying to de novo assemble transcriptome data from SOLiD using SOCs and I am can't seem to figure out what the next step is in the analysis. What do I use to visualize the results?

Also, has anyone had any success with AB's WTP?

Thanks

[westerman]

I've used ABI's WTP program a couple of times. It runs and gives something that looks like good data; e.g., a GFF file with matches and thence the counts of transcription. The accuracy of the data is unknown. Unfortunately I haven't had a separate control to do a comparison.

[SOLiD_User]

Thanks Westerman. Do you know if that was version 1.1 or 1.2 of the WTP. I've had some problems getting 1.2 to work.

[westerman]

Version 1.2 of the WTP.

My changes to the WTP have been with the '-N' (job name) option that the pipeline is trying to send to the version of PBS that our system uses. Aside from that there have been no problems. On the other hand I haven't pushed the pipeline very hard.