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Old 10-11-2015, 06:15 PM   #1
IKnowNothing
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Location: Kongo, Africa

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Default Help: Gene Copy Number for individual organism (not CNV)

Greetings!
I am trying to determine the copy number of certain genes found in an individual organism (i.e. how many copies does an organism have of 'x' gene) by using read depth analysis of WGS paired end read data. I'm extremely interested in learning if this can be done, and if so, how. I'd be incredibly thankful if anyone could help in this matter.

Last edited by IKnowNothing; 10-11-2015 at 06:17 PM.
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Old 10-12-2015, 08:16 AM   #2
JamesJoyce
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Hello, I am trying to do the same. I was told I could map to the genome and then use bedtools on the long run, but I am a little confused on how to do this. I would also be grateful if anyone could provide an answer for this.
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Old 10-12-2015, 08:20 AM   #3
GenoMax
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Here is a past thread on this topic that may be useful: http://seqanswers.com/forums/showthread.php?t=41062
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Old 10-12-2015, 01:56 PM   #4
IKnowNothing
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Thanks! Wouldn't this method only give estimated values? I was hoping to be able to use read depth analysis to find amount of gene copies... I know it's possible, but I haven't seen any examples over the web on how to do it.
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bioinformatics, coverage, gene copy number, read depth analysis, wgs

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