SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Coverage in given regions AndreaIzq Bioinformatics 1 06-20-2013 01:27 PM
Extremely high Coverage in some regions JMFA Bioinformatics 2 01-11-2013 03:42 AM
When viewing a BAM, can you specify regions of a certain coverage? oiiio Bioinformatics 3 01-10-2012 07:59 AM
Agilent SureSelect - coverage of high GC regions NGSfan Genomic Resequencing 28 11-07-2011 02:13 PM
downsampling high coverage regions in SAGs novi Bioinformatics 0 06-30-2011 02:28 AM

Reply
 
Thread Tools
Old 07-03-2013, 04:08 AM   #1
AndreaIzq
Junior Member
 
Location: Spain

Join Date: Jun 2013
Posts: 5
Default Get coverage value in given regions

Hello,
I am trying to get the normalized coverage value in some given regions (bed file) but I don't succeded. Is there any easy way to do so? I am quite new in bioinformatics, sorry for asking basic questions.

Thanks in advance,

Andrea
AndreaIzq is offline   Reply With Quote
Old 07-03-2013, 07:22 AM   #2
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

What do you mean by normalized? Do you want the raw coverage counts for different samples and then to just divide by the total number of reads? Do you want coverage of every base in a region or just the average coverage within a region? What commands have you tried to achieve this?
Heisman is offline   Reply With Quote
Old 07-03-2013, 08:20 AM   #3
AndreaIzq
Junior Member
 
Location: Spain

Join Date: Jun 2013
Posts: 5
Default

Thanks Heisman for your reply.
What I exactly want is to plot the average coverage of my proteins in several regions (bed file). In the y axis, the average coverage and in the x axis, the width of this regions.
I want to know if there is a direct relationship between the width of that regions and the coverage of my proteins. I don't know what normalized procedure to use to be able to compare the coverage of my proteins.

Thanks again,
Andrea
AndreaIzq is offline   Reply With Quote
Old 07-03-2013, 12:53 PM   #4
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

Is this an RNA-seq experiment? Have you heard the term "RPKM", and do you feel that would be appropriate regarding normalization?

I haven't worked with RNA-seq data myself so maybe someone else will chime in with a tool that can do what you want without issues.

Without incorporating any normalizing, though, if you just wanted to compute average coverage for a series of regions, I believe the easiest way to do it is described here: https://groups.google.com/forum/#!to...ss/WSNEVuHIpz0

Which shows a variant of this command:

coverageBed -abam ALIGNED_FILE.bam -b REGIONS.bed -d | groupBy -c 5 -o mean
Heisman is offline   Reply With Quote
Old 07-04-2013, 02:57 AM   #5
AndreaIzq
Junior Member
 
Location: Spain

Join Date: Jun 2013
Posts: 5
Default

That's a ChIP-Seq experiment. I wil try to do it with the average coverage as you suggested, if the results are not correct I will try RPKM then.

Thanks.
AndreaIzq is offline   Reply With Quote
Old 07-04-2013, 08:32 AM   #6
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

I have not done ChIP-seq so I may be missing something but the only thing that jumps out as obvious for normalization purposes is the number mapped reads for each sample. Good luck.
Heisman 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 02:51 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO