Which Mappability Track To Use?

Question

[Biomed]

There are a number of mappability tracks in the UCSC browser many of which have different/similar k-mer versions. I choose the ones that are similar to the k-mer lengths we use in our mapping process but my question is: What are the main issues when deciding which one of these tracks to use? Are they simply interchangeable if they have the same k-mer option? What is your heuristic to choose from among those tracks when you use them?

I would like to see if there is a relationship between the mappability of a region (as defined by the track) and the genotypes I detect using exome sequencing (illumina)

Thanks

[lh3]

Almost certainly there is a relationship. Actually you do not need a track. The mapper already tells you which region tend to be repetitive.

[Chris Miller]

Can you give more information on what you're using these mapability tracks for?

[Biomed]

I would like to see if there is a relationship between the mappability of a region (as defined by the track) and the genotypes I detect using exome sequencing (illumina)

[lh3]

Almost certainly there is a relationship.

Answer 1

[Mikael Huss]

You might want to look at this paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377

I know that there is a group (different from the one in the paper above) who are developing a general tool for generating mappability statistics for your particular genome and reads. I will update here when I hear that it has been released.

[lh3]

I briefly looked at the paper. Quite nice. I would probably go for that if I had constructed my own mask.

[Biomed]

Is this not the GEM mappability track that is available inthe UCSC genome browser? If so I guess the answer is to use the GEM track as opposed to broad, duke or Umass tracks.