need a bioinfomatics primer!

biophy6 · 02-02-2012, 06:58 AM

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 · 02-02-2012, 07:04 AM

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 · 02-02-2012, 08:05 AM

Thanks.

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

Thanks!
O

adaptivegenome · 02-02-2012, 08:28 AM

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 · 02-02-2012, 08:35 AM

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 · 02-02-2012, 08:42 AM

You are walking distance from the Broad Institute

biophy6 · 02-02-2012, 08:47 AM

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 · 02-02-2012, 12:42 PM

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 · 02-02-2012, 01:08 PM

Contact Mauricio Carneiro at 301

Joann · 02-03-2012, 01:59 PM

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

aFerrin · 02-03-2012, 02:32 PM

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 · 02-07-2012, 07:21 AM

Thanks for all the feedback.

-O

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02-02-2012, 06:58 AM	#1
biophy6 Junior Member Location: Boston Join Date: Aug 2011 Posts: 5	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

02-03-2012, 01:59 PM	#10
Joann Senior Member Location: Woodbridge CT Join Date: Oct 2008 Posts: 231	Perhaps a SEQanswers geographical community forum? Anyone, time to set up a SEQanswers geographical community forum in Boston? See post #54367 from Cambridge, UK.

02-03-2012, 02:32 PM	#11
aFerrin Junior Member Location: Rocky Mountains Join Date: Jan 2012 Posts: 1	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

02-02-2012, 07:04 AM	#2
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	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.

02-02-2012, 08:05 AM	#3
biophy6 Junior Member Location: Boston Join Date: Aug 2011 Posts: 5	Thanks. I won't be doing the analysis myself. I just need to understand the process and the associated costs. Thanks! O

02-02-2012, 08:28 AM	#4
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	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.

02-02-2012, 08:35 AM	#5
biophy6 Junior Member Location: Boston Join Date: Aug 2011 Posts: 5	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

02-02-2012, 08:42 AM	#6
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	You are walking distance from the Broad Institute

02-02-2012, 08:47 AM	#7
biophy6 Junior Member Location: Boston Join Date: Aug 2011 Posts: 5	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.

02-02-2012, 12:42 PM	#8
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	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.

02-02-2012, 01:08 PM	#9
davehsu04 Junior Member Location: san francisco Join Date: Jun 2010 Posts: 1	Contact Mauricio Carneiro at 301

02-07-2012, 07:21 AM	#12
biophy6 Junior Member Location: Boston Join Date: Aug 2011 Posts: 5	Thanks for all the feedback. -O