Originally posted by Xi Wang
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Thank you very much for the reply. I was referring to the 5th column. It IS the mapping quality according to SAM manual. But I guess this mapping quality must be correlated with alignment score for some way.
I have seen a lot of alignment with low mapping quality (0 or 1). For the input of cufflinks, do you usually filter out these low quality mapping reads? what is the cutoff you usually use?
Thanks
Originally posted by Haneko View PostHi there,
That is actually not the score, but the mapping quality (I'm assuming you're referring to column 5 for 255 "score"). For calculation of score, you will have to take the alignment in colorspace (XL:Z) and the number of colorspace mismatches (XU:Z), then use SOLiD's formula.
A score of 10 shouldn't be appearing in the output. The seed of 25bp mapping with at most 2 mismatches will give u the lowest possible score for an alignment to be reported, which in my case is 18.
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Hi clariet,
Actually I've never considered this column to be a factor in filtering, so i can't give you a definite answer. But I think it'd be good to filter away those low quality mappings, perhaps someone could give a recommendation on the threshold?
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