Fastq quliaty score and MAQ output quality score

baohua100 · 02-18-2009, 10:03 PM

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

swbarnes2 · 02-19-2009, 10:21 AM

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
454 quality score, z-score,..	nii	454 Pyrosequencing	4	10-15-2020 07:29 AM
Detecting FASTQ Quality Score Format	bhan	Bioinformatics	2	01-02-2012 04:40 PM
Meaning of '0' quality score in MAQ	paulig	Bioinformatics	0	11-29-2010 07:33 AM
Threshold quality score to determine the quality read of ILLUMINA reads problem	edge	General	1	09-13-2010 03:22 PM
ELAND output quality score	kwtennis311	Bioinformatics	0	06-30-2010 10:51 AM

02-18-2009, 10:03 PM	#1
baohua100 Senior Member Location: Canada Join Date: Jun 2008 Posts: 103	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

02-19-2009, 10:21 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	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.