SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Show filtered reads in the IGV? MBender Bioinformatics 0 01-25-2012 01:04 PM
Black line between two reads in IGV kasthuri Bioinformatics 3 01-13-2012 06:32 AM
RTG Investigator variant detection white paper Stewart Noyce Vendor Forum 0 06-30-2011 09:27 AM
missing reads in IGV display cswarth Bioinformatics 2 06-28-2011 09:30 AM
Greetings from a grey zone YohnTheViking Introductions 0 04-19-2010 01:36 AM

Reply
 
Thread Tools
Old 08-03-2011, 01:44 AM   #1
ocs
Member
 
Location: Berlin, Germany

Join Date: May 2011
Posts: 27
Default IGV reads (grey vs white)

Hello folks,

concerning the Integrative Genomics Viewer:
What is the difference between the white and the grey reads? Some reads in the alignment are all filled with grey and some are outlined with grey but filled with white. I couldn't find any answer in the manual (http://www.broadinstitute.org/softwa.../AlignmentData).

Thanks in advance,
best regards,
Oliver
ocs is offline   Reply With Quote
Old 08-03-2011, 02:07 AM   #2
Seq84
Member
 
Location: Italy

Join Date: Feb 2011
Posts: 19
Default

Hi,
Reads filled with white have mapping quality score = 0
best regards,
Matteo
Seq84 is offline   Reply With Quote
Old 08-03-2011, 02:28 AM   #3
ocs
Member
 
Location: Berlin, Germany

Join Date: May 2011
Posts: 27
Default

Thanks!
Does this mean that they are aligned just by desperation?
ocs is offline   Reply With Quote
Old 08-03-2011, 06:42 AM   #4
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

It usually means there are two or more equally likely locations, and so this location was randomly chosen from that set.
nilshomer is offline   Reply With Quote
Old 08-03-2011, 06:52 AM   #5
ocs
Member
 
Location: Berlin, Germany

Join Date: May 2011
Posts: 27
Default

Hello nilshomer,

thanks for your answer. Its a bit confusing, I can think of two equally likly locations that both have a great mapping quality but then its set to zero because its ambiguous?
ocs is offline   Reply With Quote
Old 08-04-2011, 05:27 AM   #6
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

First apologies this was not documented, we'll correct that. I agree its confusing, I think ambiguous mappings should be indicated by a separate score or field, but that's the way it is.

Jim
Jim Robinson is offline   Reply With Quote
Old 06-13-2012, 08:57 AM   #7
Orr Shomroni
Member
 
Location: Netherlands

Join Date: Oct 2011
Posts: 26
Default

Hello everyone,

To continue on this grey vs. white issue, I have an IGV plot containing 2 reads: 1 long at a certain position, and another slightly shorter which is one position afterwards (i.e. in terms of positions, the small read is contained within the range of the big read). In IGV, the big read is marked white (i.e. can be aligned elsewhere), the small is grey, and the big read has no SNPs/Indels in its edges. The question is, how is it possible that a certain read can be aligned to multiple positions, whereas its subsequence is unique?
On the same note, which tool determines whether a read can be mapped to multiple locations (i.e. white bar)? Can IGV calculate that itself?
__________________
"Though it may seem that all's been said and done, originality still lives on" - some unoriginal guy who had nothing better to write as his signature
Orr Shomroni is offline   Reply With Quote
Old 06-13-2012, 10:22 AM   #8
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Hi,

IGV is not making any judgement calls, is is using the mapping quality. It is a convention with at least some aligners (BWA), if not all aligners, that mapping quality == 0 means the read is not uniquely mapped. IGV does not do any calculation. So if you want to take all interpretation out of the picture a "white" read simply means that the mapping quality has been set to zero by the aligner.

Jim
Jim Robinson 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 06:40 AM.


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