SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Detecting FASTQ Quality Score Format bhan Bioinformatics 2 01-02-2012 03:40 PM
454 quality score, z-score,.. nii 454 Pyrosequencing 2 10-14-2011 09:46 AM
Meaning of '0' quality score in MAQ paulig Bioinformatics 0 11-29-2010 06:33 AM
Threshold quality score to determine the quality read of ILLUMINA reads problem edge General 1 09-13-2010 02:22 PM
ELAND output quality score kwtennis311 Bioinformatics 0 06-30-2010 09:51 AM

Reply
 
Thread Tools
Old 02-18-2009, 09:03 PM   #1
baohua100
Senior Member
 
Location: Canada

Join Date: Jun 2008
Posts: 103
Default Fastq quliaty score and MAQ output quality score

fastq file:
@I326_2_FC306FCAAXX:8:1:50:985
ATGTCCGAAGGGCAGTCTCAAGTGGTAAAATGGAT
+I326_2_FC306FCAAXX:8:1:50:985
hhhWhhhchhhhhahShh\PO]LgXZXPNLUTZNO


MAQ alignment output:

I326_2_FC306FCAAXX:8:1:50:985 1 1 + 0 0 99 99 99 0 0 1 0 35 ATGTCCGAAGGGCAGTCTCAAGTGGTAAAATGGAT ```W```````````S``\PO]L`XZXPNLUTZNO

what's the meaning of ```W```````````S``\PO]L`XZXPNLUTZNO ?

not the same as hhhWhhhchhhhhahShh\PO]LgXZXPNLUTZNO
baohua100 is offline   Reply With Quote
Old 02-19-2009, 09:21 AM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Well, they actually look pretty similar, the first one is maintaining distinctions between the quality of 7th and 8th letters, for instance, while Maq is treating them the same.

Is it possible that your fastq is flipped in orientation, and those are the low quality letters first? Maybe the first one is splitting out the low quality scores much finer than Maq.
swbarnes2 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 12:17 PM.


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