What's your favorite way to analyze your data?

[farrel75]

So imagine I have a FASTA file from my assembly run on the Miseq. As I am completely unfamiliar with anything to do with downstream analysis or the various software, I don't know what to do with the data. So...what's your favorite thing to do with it? What should I do? I assume I need to put all the reads together somehow. So please fill me with your knowledge oh wise ones!

[westerman]

ABySS.

But there are other genome sequencers as well. Some tuned to different branches of life; e.g., those oriented towards bacterial assembly.

I suggest reading the forum. Lots of information in it.

[Mark]

While redirecting it to /dev/null will save you alot of disk space and headaches, it may upset the PI.
Your question is much too vague. Define the purpose of the study then seek out tools.

[TiborNagy]

Every analysis should be a goal and I choose programs that fits to it. What is your aim?

[adaptivegenome]

While redirecting it to /dev/null will save you alot of disk space and headaches, it may upset the PI.
Your question is much too vague. Define the purpose of the study then seek out tools.

A great suggestion especially for those that do not know why they did an experiment in the first place...

[farrel75]

To be fair, I wasn't too sure of the goal myself. What we did was whole genome sequencing with a lot of genomes (E. coli, L. reuterii, and C. difficile). This was more of a trial thing to try out the MiSeq so there wasn't really a goal involved. Basically, I'm supposed to run it and play with the data to figure out what I can do with it.

I guess the questions are what is a good assembler for bacterial genomes? Right now I'm playing around with Velvet but I want to see what else is out there. So does anyone have any suggestions on what I could try out?

Also, anyone a big fan of mapping and wanting to rave about their favorite program for it?

[TiborNagy]

I like MIRA for assembling bacterial genomes, because it has some hybrid assembling methods.

[Mark]

Why don't you start with the MiSeq's onboard analysis tools (velvet, BWA, etc) , then move to the standalone version's of these to see what the increased ability to parameterize these tools can do for you, and then perhaps move on to other tools.