RNA-seq with No Reference Genome

[taylormjeffery]

Hello community,

I'm new to the genome sequencing game, though I do have a fairly good understanding of genetics and the technology. I'm currently researching glyphosate resistant Giant Ragweed, for which there is NO reference genome, or a reference genome of any reasonably closely related species.

I'm currently enrolled in my 3rd semester of my MSc. I'd like to use RNA-seq as a means of discovering genes that might be involved in the resistance response. Ideally i'd like to do a pairwise comparison of a mature resistant leaf against a susceptible one, as well as a comparison between a unsprayed mature resistant leaf and a sprayed one. The contact I have for the sequencing would be using the Illumina HiSeq platform.

So I have a few questions:
1. Given that a MSc is supposed to be 6 semesters, is this possible or should I consider switching into a PhD?
2. Is this possible at all?
3. Can you recommend software capable of this kind of analysis and how much computing power and RAM will I need to do this (in a reasonable amount of time)?
4. Does anyone know of a giant ragweend genome or closely related genome that I may be unaware of?

Thanks everyone for your help,
Taylor Jeffery

[mbblack]

Honestly, that's one huge bite to chew off for a M.Sc., in my opinion. You'll need to do your own de nova assembly from transcript data. Given you are already half way through your masters tenure, there is no way you can complete that project in 3 semesters, IMO.

Have a look at:
Manfred G Grabherr, et. al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644–652