SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
seq.txt, qseq.txt and fastq NicoBxl Bioinformatics 5 01-03-2014 09:35 AM
How to make sense of Tophat's output file 'junctions.bed' gsinghal RNA Sequencing 4 09-03-2012 07:49 AM
export.txt files/ quality filtering oleg Illumina/Solexa 8 08-19-2010 06:20 AM
qseq files versus sequence.txt files drio Illumina/Solexa 3 11-09-2009 10:02 AM
quality scores vs prb files Leighton Illumina/Solexa 7 10-16-2008 02:58 AM

Reply
 
Thread Tools
Old 04-27-2009, 04:35 PM   #1
TylerBackman
Member
 
Location: Riverside, CA

Join Date: Oct 2008
Posts: 13
Default Can anyone make sense of the quality scores in the qseq.txt files?

I'm running the Illumina pipeline 1.3.2, and I noticed that the quality scores in the qseq.txt file appear to be the same as the alignment-normalized scores produced by Eland/Gerald, which are totally erroneous for reads without a good reference genome.

It seems like Gerald is going back and injecting these quality scores into the Bustard output rather than just putting them in the Gerald output. Why would they do this? Is there any way to get the quality scores in the new (Phred) format without producing the legacy prb files and converting them?
__________________
@1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
""""""""""""""""""""""""""""""""""""
TylerBackman is offline   Reply With Quote
Old 04-29-2009, 06:08 AM   #2
dcjamison
Member
 
Location: Cincinnati

Join Date: Oct 2008
Posts: 15
Default

As of 1.3.2, Bustard does the qs calibration according to an internal table. You can do custom calibration from the command line, so if you want uncalibrated scores in the new format you could create probably create a custom custom calibration table that leaves the values unchanged. I do not know the format of the calibration table off the top of my head, but it is somewhere in the distribution.
dcjamison is offline   Reply With Quote
Old 04-29-2009, 10:23 AM   #3
TylerBackman
Member
 
Location: Riverside, CA

Join Date: Oct 2008
Posts: 13
Default

So calibration no longer depends on the reference genome?

If so, this makes a lot of sense, as it doesn't make the (often false) assumption that all failed alignments are due to sequencing error.

Quote:
Originally Posted by dcjamison View Post
As of 1.3.2, Bustard does the qs calibration according to an internal table. You can do custom calibration from the command line, so if you want uncalibrated scores in the new format you could create probably create a custom custom calibration table that leaves the values unchanged. I do not know the format of the calibration table off the top of my head, but it is somewhere in the distribution.
__________________
@1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
""""""""""""""""""""""""""""""""""""
TylerBackman 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 04:28 AM.


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