Meaning Of '0' Quality Score In Maq?
1
2
Entering edit mode
12.0 years ago
Paul ▴ 760

If a read has a zero quality score in MAQ does that mean:

a) The read aligns to multiple positions b) The read aligns to nowhere

I think it's either one or both of these but I'd hope someone can clear it up for me?

quality • 3.7k views
ADD COMMENT
7
Entering edit mode
12.0 years ago
User 59 13k

It means the reads map to multiple positions in this case - equally well.

And a quick check of the MAQ FAQ would have shown this:

"What happens to the reads that can be mapped to many positions?

If a read can be mapped to several equally best positions, Maq will randomly choose one position and give the alignment a zero mapping quality."

ADD COMMENT
1
Entering edit mode

Well they could be from paralagous genes or repetitive sequences. It's kind of hard to just make a general rule on non-specific matches. Have a read of this: http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html

ADD REPLY
0
Entering edit mode

Oh right, dunno how I missed that, is there really any point in filtering these out if this is the case? I'm analyzing some rna-seq data.

ADD REPLY

Login before adding your answer.

Traffic: 1286 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6