Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD

Similar Threads
Thread Thread Starter Forum Replies Last Post
what is the meaning of BED score? whfwind Bioinformatics 3 07-24-2017 10:45 PM
What is the meaning density in CummeRbund plots? Carlos Borroto Bioinformatics 16 12-29-2016 09:05 PM
the meaning of sequence 'M','Y','K' in samtools? dkrtndhkd Bioinformatics 2 02-05-2012 11:56 PM
Meaning of '0' quality score in MAQ paulig Bioinformatics 0 11-29-2010 06:33 AM
the meaning of Match Position for reads? beliefbio Illumina/Solexa 2 11-27-2009 05:43 PM

Thread Tools
Old 01-22-2009, 12:57 PM   #1
Junior Member
Location: houston

Join Date: Jan 2009
Posts: 1
Default What is the meaning of quality value?

In the XXXX_.QV.qual file, there is a quality value for each position.

I wonder how they calculate this value and what is the meaning of this value.

For traditional sequecing, I think quality value is the P value of the corret read over the noise, then -10logP. However, for SOLID, every read is from 2 base pair, how do they get the quality value? Anybody can provide some advice or reference?

Thanks a lot!
lowfat is offline   Reply With Quote
Old 01-22-2009, 11:34 PM   #2
Location: India

Join Date: Oct 2008
Posts: 36

I think it gives quality value for color call...this is abased many parameters majorly intensity.
Rao is offline   Reply With Quote
Old 02-02-2009, 04:02 PM   #3
Mr Mutundes
Location: Sydney, Australia

Join Date: Jan 2009
Posts: 17

This is all I have been able to find:

"The QV value is calculated using a phred like score
q = -10 x log10(p)
where q is the quality value and (p) is the predicted probability that the color call is incorrect"

which is from this document:
Mr Mutundes is offline   Reply With Quote
Old 10-21-2009, 03:53 PM   #4
Location: New York City

Join Date: Aug 2009
Posts: 14

If you convert from colorspace to [ATGC], how do you convert the QV value? Take the average?
juan is offline   Reply With Quote
Old 10-26-2009, 12:20 PM   #5
Senior Member
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,315

Originally Posted by juan View Post
If you convert from colorspace to [ATGC], how do you convert the QV value? Take the average?
No, that would not be right.
I recommend against conversion of raw reads from color space because an error in one position would propagate through the rest of the read. That is, if your read had a single error at base 2, then by converting the read to base space, you would ensure that every base after base 2 was incorrect.

Later errors could shift you back into the correct sequence frame, however. So, even were you wanting to risk switching into base space, there would be no way to convert the quality values. Or at least, no trivial way.

On the other hand, converting base space sequence into color space involves no such risk. Converting quality values would still not be straight forward, but you could estimate them by choosing the lower quality value of the two bases.

Really, if you are trying to use color space-naive code, your only decent choice is to use "double encoding". This involves doing a tr/0123/acgt/ conversion. The resulting fake sequence now is usable in color space-naive code. With the caveat that reverse-complementing is illegitimate on double encoded sequence. (Because in color space one reverses to reverse-complement...)

pmiguel is offline   Reply With Quote


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 04:17 AM.

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