SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Read coverage for each gene migs54 Bioinformatics 6 04-21-2015 03:44 PM
Average Read Coverage for 454 paired end read data lisa1102 Core Facilities 8 10-18-2011 08:40 AM
1/2 read and coverage? Triticum 454 Pyrosequencing 3 09-08-2009 07:13 AM
The coverage of re-sequencing sample ptongyoo General 1 05-19-2009 03:33 AM
Sample short read data set? ECO Bioinformatics 9 02-28-2008 06:53 PM

Reply
 
Thread Tools
Old 06-17-2013, 06:52 AM   #1
sadiexiaoyu
Member
 
Location: Switzerland

Join Date: Apr 2013
Posts: 55
Default why different read coverage in the same gene in one sample

Hi, All,

I am using IGV to view my bam result. And I am confused why there are different read coverage in the same gene. I mean, ideally, the read coverage should be even across the gene. But in some cases (for example, see the two attachments), I found the read coverage is significant difference across gene. Could anyone help explain this? Thanks!

Best,

Sadiexiaoyu
Attached Files
File Type: pdf g .pdf (70.6 KB, 13 views)
File Type: pdf f .pdf (44.1 KB, 7 views)
sadiexiaoyu is offline   Reply With Quote
Old 06-17-2013, 07:00 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

This is normal. Firstly, "random hexamer priming" is actually not that random. That leads to a lot of the waviness that you see. Secondly, there are also 5' to 3' biases, caused be the library construction step and RNA degradation. There are also mapability differences across the length of a gene (which can interact with the SNPs that are present in samples).
dpryan is offline   Reply With Quote
Old 06-17-2013, 11:44 PM   #3
sadiexiaoyu
Member
 
Location: Switzerland

Join Date: Apr 2013
Posts: 55
Default

Quote:
Originally Posted by dpryan View Post
This is normal. Firstly, "random hexamer priming" is actually not that random. That leads to a lot of the waviness that you see. Secondly, there are also 5' to 3' biases, caused be the library construction step and RNA degradation. There are also mapability differences across the length of a gene (which can interact with the SNPs that are present in samples).
Hi, dpryan,

Thanks!

Best,

Sadiexiaoyu
sadiexiaoyu 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 05:00 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO