SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to find inner mean distance and standard deviation in Galaxy skmotay RNA Sequencing 0 11-05-2014 05:40 PM
How to calculate standard deviation between replicate in mRNA seq data? rahulvibes RNA Sequencing 0 07-28-2014 07:25 AM
Cufflinks' estimated fragment length mean and standard deviation d f Bioinformatics 12 01-18-2014 10:32 AM
SOAPdenovo2 standard deviation input? Petrichor Bioinformatics 1 05-13-2013 11:18 PM
Insert size standard deviation phlojo Illumina/Solexa 2 09-14-2012 08:24 AM

Reply
 
Thread Tools
Old 07-12-2015, 06:44 AM   #1
shmibble
Member
 
Location: Israel

Join Date: May 2015
Posts: 23
Default Qualimap Large Standard Deviation

Hi,

I'm using Qualimap for quality control in a pipeline.
Under "Coverage" I get a standard deviation that is larger than the mean value. This seems a little suspicious. Does this mean there is likely some sort of problem?

Thanks for the help
shmibble is offline   Reply With Quote
Old 07-12-2015, 08:40 AM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

I've never used Qualimap, but it's not unusual to have a standard deviation larger than the mean, depending on your experiment. Particularly with single-cell, or LMP libraries, or anything over-amplified, or other protocols that are expected to be highly biased. Can you give more details?
Brian Bushnell is offline   Reply With Quote
Old 07-15-2015, 11:15 PM   #3
shmibble
Member
 
Location: Israel

Join Date: May 2015
Posts: 23
Default

Thanks for the reply.
I am amplifying certain areas more than others. So that might be the issue.
As I am still no expert in this, What would you recommend other than Qualimap?
shmibble is offline   Reply With Quote
Old 07-16-2015, 10:40 AM   #4
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

Before I can recommend something, I'd need to know exactly what you're trying to measure. BBMap can generate the standard deviation and average coverage, but there's no reason to expect it would give a different answer. You are running an experiment with intentionally uneven coverage, so when you analyze the coverage and find that it is uneven, that should be what you expect.
Brian Bushnell is offline   Reply With Quote
Old 07-18-2015, 11:08 PM   #5
shmibble
Member
 
Location: Israel

Join Date: May 2015
Posts: 23
Default

You're right. I guess I didn't think about that before. I don't really need a different program then.

Thanks!
shmibble is offline   Reply With Quote
Reply

Tags
qualimap, quality control

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 03:38 AM.


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