BINF 6215: RNA-Seq in CLC Genomics

OK — we’ve done a few exercises now where everything’s spelled out for you — this time you’re on your own.  You have access to a variety of bacterial RNA-Seq data sets. Legitimate things to do with transcriptomes include:

• Differential expression analysis — parts (1)(2)(3)
• de novo assembly and analysis
• Discovery of novel transcripts

While we don’t have the Blast2Go tool that is used in the second tutorial, you can add the (beta) transcript discovery plugin via the plugins interface.

We’ll discuss the steps as a group before you try to implement. Your goal — to get as much of the work into an automated workflow as possible. Some steps may not be workflow-able; discover which these are and make a note of where you have to complete analyses manually. Some of those steps may be workflow-able in another context, like BioExtract or Galaxy, or at the command line.