need a bioinfomatics primer!

[biophy6]

Hi all,

I'm totally new to the whole world of sequencing and I am trying to understand the overall process AFTER sequencing - mutation calling, annotation, interpretation. Can anyone direct me to a basic primer on the subject?

What I really want to understand is - what software packages and services exist to solve these problems and what are the general costs and prices.

Thanks!

-O

[adaptivegenome]

I am moving this to the General section. Try taking a look at the GATK Best Practices v3 if you are going to do the analysis yourself.

[biophy6]

Thanks.

I won't be doing the analysis myself. I just need to understand the process and the associated costs.

Thanks!
O

[adaptivegenome]

The costs vary depending on whether you work with a company or academic core. And the costs depends very much on what you want to do.

[biophy6]

I looked at the GATK. Looks like I need more remedial help.

Is anyone in the Kendall Square, Cambridge, MA area willing to sit & explain the process to me? We can meet at a cafe and I'll pay for the coffee/snacks. I'm starting way at the beginning. I have a background in science, but not genetics.

Thanks!

O

[adaptivegenome]

You are walking distance from the Broad Institute

[biophy6]

That's the sad thing!

I WORK at the Broad Institute. I was hoping to meet some friendly Broadies and non-Broadies on this forum to help me out.

[westerman]

No wanna-be Broadies? :-)

As genericforms points out, the costs and programs and methods very much depend on what you want to do. There are many different experiments and goals that can be done with NGS. I break out the work into 3 initial broad categories:

Genome-wide analysis
Transcriptomes (rnaseq)
Amplicon

Then depending on if you have reference sequence the former two can be broken down into

de-novo
versus a reference

And depending on the number of samples you might want to do comparative studies between your samples and other people's samples. Almost always want to do this for transcriptome and amplicon studies.

But those are just really broad concepts. If you want an expert on de-novo transcriptome then get hold of Brian Haas at the Broad. He is one of the main authors of the Trinity package.

[davehsu04]

Contact Mauricio Carneiro at 301

[Joann]

Perhaps a SEQanswers geographical community forum?

Anyone, time to set up a SEQanswers geographical community forum in Boston?
See post #54367 from Cambridge, UK.

[aFerrin]

Golden Helix has an interesting NGS primer on their blog site, in three parts (A Hitchhiker’s Guide to Next Generation Sequencing). Not sure if it is what you are looking for, but it's worth a shot.

http://blog.goldenhelix.com/?p=423

Andy

[biophy6]

Thanks for all the feedback.

-O