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Old 02-02-2012, 06:58 AM   #1
biophy6
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Default need a bioinfomatics primer!

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
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Old 02-02-2012, 07:04 AM   #2
adaptivegenome
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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.
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Old 02-02-2012, 08:05 AM   #3
biophy6
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Thanks.

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

Thanks!
O
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Old 02-02-2012, 08:28 AM   #4
adaptivegenome
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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.
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Old 02-02-2012, 08:35 AM   #5
biophy6
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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
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Old 02-02-2012, 08:42 AM   #6
adaptivegenome
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You are walking distance from the Broad Institute
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Old 02-02-2012, 08:47 AM   #7
biophy6
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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.
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Old 02-02-2012, 12:42 PM   #8
westerman
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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.
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Old 02-02-2012, 01:08 PM   #9
davehsu04
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Contact Mauricio Carneiro at 301
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Old 02-03-2012, 01:59 PM   #10
Joann
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Default Perhaps a SEQanswers geographical community forum?

Anyone, time to set up a SEQanswers geographical community forum in Boston?
See post #54367 from Cambridge, UK.
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Old 02-03-2012, 02:32 PM   #11
aFerrin
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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

Last edited by aFerrin; 02-03-2012 at 02:35 PM. Reason: added link
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Old 02-07-2012, 07:21 AM   #12
biophy6
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Thanks for all the feedback.

-O
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