Grad Student in way over my head!

snowkat · 12-07-2010, 08:54 AM

Hi,
I'm new here. Just trying to get my bearings to see what I can find out about using paired end reads to detect structural variation in tumor genomes. I know it can be done... just not sure what path to take and whether or not I can do it myself or if I will need to find someone to collaborate with.

Cheers!
Kathy

husamia · 12-07-2010, 11:23 AM

are you referring to human genomes? you need to narrow down little bit your target of interest. its difficult to screen entire genome for structural variants and how many samples are you considering?

snowkat · 12-07-2010, 11:27 AM

Hi,
We are interrogating the mouse genome using paired end mapping. We want to find new translocation junctions... so narrowing regions or enriching would prohibit that. We are looking at running a handful of samples, up to 10.
Are you thinking I am going to have problems with this approach?

NextGenSeq · 12-07-2010, 11:59 AM

I think your approach is fine if you can afford it. The analysis might be difficult though.

frozenlyse · 12-07-2010, 03:21 PM

I saw a talk from a guy from the Sanger who does this routinely in human clinical samples - they say they (pretty much) find all structural variants by fragmenting DNA to 600bp and then running 2 lanes of 50bp PE sequencing on a HiSeq

snowkat · 12-07-2010, 04:10 PM

Quote:

Originally Posted by NextGenSeq

I think your approach is fine if you can afford it. The analysis might be difficult though.

I have read that there are programs (such as PEMer) that can help with the analysis... any experience with it? Heard any horror stories?

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12-07-2010, 08:54 AM	#1
snowkat Junior Member Location: Maine Join Date: Dec 2010 Posts: 3	Grad Student in way over my head! Hi, I'm new here. Just trying to get my bearings to see what I can find out about using paired end reads to detect structural variation in tumor genomes. I know it can be done... just not sure what path to take and whether or not I can do it myself or if I will need to find someone to collaborate with. Cheers! Kathy

12-07-2010, 11:23 AM	#2
husamia Member Location: cinci Join Date: Apr 2010 Posts: 66	are you referring to human genomes? you need to narrow down little bit your target of interest. its difficult to screen entire genome for structural variants and how many samples are you considering?

12-07-2010, 11:27 AM	#3
snowkat Junior Member Location: Maine Join Date: Dec 2010 Posts: 3	Hi, We are interrogating the mouse genome using paired end mapping. We want to find new translocation junctions... so narrowing regions or enriching would prohibit that. We are looking at running a handful of samples, up to 10. Are you thinking I am going to have problems with this approach?

12-07-2010, 11:59 AM	#4
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	I think your approach is fine if you can afford it. The analysis might be difficult though.

12-07-2010, 03:21 PM	#5
frozenlyse Senior Member Location: Australia Join Date: Sep 2008 Posts: 136	I saw a talk from a guy from the Sanger who does this routinely in human clinical samples - they say they (pretty much) find all structural variants by fragmenting DNA to 600bp and then running 2 lanes of 50bp PE sequencing on a HiSeq