New to Next Gen not sure where to go from here

[westerman]

4 lanes should give some useful data. Use Trinity to assemble the transcriptomes. Use blast and perhaps something like blast2go for annotation.

I can't give out details but I am 100% sure that you will find potential differential Catalase and CU-SOD1 activity. I agree with dpryan that listing numbers in your thesis would not be interesting. However such numbers can be obtained if you really want them.

Good luck with the analysis. Expect a high learning curve but with, it is to be hoped, a high payback.

[dpryan]

1) As vivek alluded, if you're thinking of doing some RNAseq, then you'll need to do assembly. Knowing absolutely nothing about this, I would think an interesting experiment would be to compare glyphosate resistant vs. glyphosate sensitive ragweed, but without a reference genome/transcriptome you might need more sequencing capacity to do that easily in one shot (hopefully someone who does assembly can chime in). BTW, if a related plant has been sequenced, you might have luck aligning to that (I haven't a clue how related the various plants are, I work on mice and humans!). This is particularly true for transcriptome alignments, since there's selective pressure on that.
2) After assembly, you'll have to blast the various contigs to try to figure out what they are. Presumably you'll pick up the genes that you're most interested in. There's no great way to search the raw alignments for just a few genes, you'll likely end up getting a lot of false-positive matches.
3) Just a listing of some various quality metrics probably wouldn't be interesting enough for inclusion in a thesis, at least without knowing the exact thesis topic.

[vivek_]

http://trinityrnaseq.sourceforge.net/

Looks like a good place to start for transcriptome assembly.

[tjeffe01]

Hello all,

My supervisor and I recently jumped on the next gen bandwagon. Another professor in our department purchased lanes on an RNAseq plate and couldn't fill the entire thing so we took 4 spots. We are working on glyphosate resistant giant ragweed; for which there is no reference genome and little to no genetic data available.

We have a few questions:
1) What do you recommend we do now?
2) In addition to the whole transcriptome date we are also interested specifically in looking at the expression of two or three genes (Catalase, SOD1 Cu/Zn, and EPSPS) however we don't have giant ragweed sequences for those genes. Can we search our data for those genes and their expression levels or is that just out of the question?
3) This data will not be in my MSc and I won't be doing much work with it beyond posting here; but I would like to include a short section in my thesis on the data we collect here. Is it possible to get average read lengths, fold number and other quality statistics about the data to include in my thesis, or does that not make any sense?

Thanks everyone,
Taylor