SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Newbie Question: Calculating physical coverage from genome coverage tristanstoeber Illumina/Solexa 4 06-24-2013 11:53 AM
Calculating average coverage wih Pysam Martino Bioinformatics 1 05-29-2012 05:33 AM
calculating the coverage lyz1030 Bioinformatics 3 04-03-2012 06:03 PM
what program can i use for calculating coverage? dkrtndhkd Bioinformatics 2 02-03-2012 06:39 PM
Gene list for calculating coverage nseh Bioinformatics 1 05-22-2011 07:31 AM

Reply
 
Thread Tools
Old 05-31-2012, 05:46 PM   #1
kjaja
Member
 
Location: NY

Join Date: Aug 2011
Posts: 55
Default calculating the coverage over a gene

Hi,

I am interested in knowing the mean coverage for a specific region (for example a gene). Is this possible to calculate? If so how ?

Thanks for your help…
kjaja is offline   Reply With Quote
Old 05-31-2012, 05:50 PM   #2
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

From what type of file? This is something you can almost certainly find with just a tiny bit of searching!
ECO is offline   Reply With Quote
Old 05-31-2012, 07:15 PM   #3
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

And with the new forum feature you probably saw some threads pop up when you were creating this one that are relevant.

It does depend on your type of file, but you might want to look into GATK DepthOfCoverage.
Heisman is offline   Reply With Quote
Old 06-01-2012, 07:01 AM   #4
azneto
Member
 
Location: Brazil

Join Date: Dec 2009
Posts: 24
Default

The questions from ECO are really important in order to answer that.
In anyways, I'm having really good results using Bedtools (http://code.google.com/p/bedtools/).
There's this 'coverageBed' tool that allows one to calculate the coverage of features within a GFF/BED file based on a mapping file (BAM).
azneto is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO