Dec 2nd, 2024 at 11:58pm
 Choose Language:
 
  Welcome, Guest. Please Login or Register
 UGENE Bulletin Board
  Welcome to our forum.
 
  HomeHelpSearchLoginRegister  
 
 
  UGENE Forum › General Category › Feature Requests › How to export base-by-base alignment coverage data?
‹ Previous Topic | Next Topic ›
Page Index Toggle Pages: 1
How to export base-by-base alignment coverage data? (Read 13378 times)
Dec 15th, 2012 at 2:57am

brianm   Offline
YaBB Newbies

Posts: 1
 *
 
I've aligned sequences to a reference and would like to output a table that shows the depth of coverage at each position using the reference sequence base numbering.
 
Back to top 
IP Logged
 
Reply #1 - Dec 17th, 2012 at 5:43pm

Yuriy Vaskin   Offline
Global Moderator

Gender: male
 Posts: 138
 *****
 
There is no way to export such information. Only visualization is available yet. But we already planned to implement it (https://ugene.unipro.ru/tracker/browse/UGENE-453)
 
Back to top 
IP Logged
 
Reply #2 - Apr 2nd, 2014 at 6:39am

Adam   Offline
YaBB Newbies

Posts: 2
 *
 
Is there a work around for this? I'd really like a list of reference positions in one column, and coverage depth in a second column.
 
Back to top 
IP Logged
 
Reply #3 - May 9th, 2014 at 3:19pm

Yuriy Vaskin   Offline
Global Moderator

Gender: male
 Posts: 138
 *****
 
We integrated bedtools genomeCov which has a number of options to show the coverage. It will be available in the next releases
 
Back to top 
IP Logged
 
Page Index Toggle Pages: 1
‹ Previous Topic | Next Topic ›
  « Home ‹ Board Top of this page

UGENE Forum » Powered by YaBB 2.5 AE!
YaBB Forum Software © 2000-2010. All Rights Reserved.

Valid RSS Valid XHTML Valid CSS Powered by Perl Source Forge