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Old 12-12-2008, 12:44 PM   #1
AnamikaDarwin
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Question Assess the quality of solexa reads

Hello,

How can you assess the quality of solexa reads?

Thanks,
AnamikaDarwin
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Old 12-13-2008, 10:10 AM   #2
Stegger
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Hi Anamika,
if you look into your sig2.txt files I believe that you can see the raw scores which I guess you can translate into quality.
In every line you have first the lane number, then tile & coordinates, and after that comes the raw data with scores from each imaging round (in the order A, C, G, & T).
If you look into the prb.txt file you will get the analysis score that the Solexa software calculated. Scores range from -40 to 40 again in the order as above.

If you are looking to get an overview of the general scores instead of looking at selected ones individually... I dont know, unfortunatly.

Hope that helps!

Last edited by Stegger; 12-13-2008 at 10:16 AM.
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Old 12-14-2008, 02:26 AM   #3
BaCh
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The analysis scores are a good start. Unfortunately, they won't show you the whole story and you might need to do some further magic.

For example, I've seen bacterial projects where a low single digit percent of the reads were all "AAAAAAAAAAAAAAAAAAAAA..." with quality analysis scores of 40 (best score). Less frequently were reads all C, G or T. As variation thereof, there were reads good up to a certain point and then incorporating only a single type of bases ... all at good quality.

The thing is: the bacteria I worked on do not contain this sequences! These are sequencing artefacts which are difficult to asses only with analysis scores.

So, for bacteria I also filter out reads that are all A, C, G, T. Then again, eukaryotesmight have poly-A / poly-T that are this long ... it's abit of a problem.

Regards,
Bastien
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Old 12-14-2008, 02:52 AM   #4
cgb
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some of your sequences are artifacts of poor image quality, flowcell imperfections etc. in which case you need to use X,Y co-ordinates as part of your filtering - and/or cross check the images.
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Old 12-15-2008, 01:35 PM   #5
AnamikaDarwin
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Quote:
Originally Posted by Stegger View Post
Hi Anamika,
if you look into your sig2.txt files I believe that you can see the raw scores which I guess you can translate into quality.
In every line you have first the lane number, then tile & coordinates, and after that comes the raw data with scores from each imaging round (in the order A, C, G, & T).
If you look into the prb.txt file you will get the analysis score that the Solexa software calculated. Scores range from -40 to 40 again in the order as above.

If you are looking to get an overview of the general scores instead of looking at selected ones individually... I dont know, unfortunatly.

Hope that helps!
Thanks Stegger,

I AM looking to getting an overview of of SOLEXA read qualities. I would like to be able to discern the qualities of those reads that are aligning with my reference using MAQ.

Anamika
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