Calculate mappability for an interval?

[Vasilisa]

Hi all,

I downloaded the mappability file from here:
ftp://encodeftp.cse.ucsc.edu/pipelin...odeMapability/

then I coverted it into bedGraph format using bigWigToBedGraph.
It looks like this:

chr1 10000 10090 0.000668896
chr1 10090 10091 0.000847458
chr1 10091 10093 0.00107411
chr1 10093 10096 0.00719424
...

My questions are:
1) why the distances between start and end positions are not equal? For example, 10090-10000=90 and 10093-10091=2
2) how do I calculate mappability for an interval? Let's say, I want to know the mappability of a region 10000 - 10096, how should I treat the scores for intermdiate positions?



Thanks in advance for the explanation!
Vasilisa

[Jonathan87]

Because if position i until position i+90 all have the same pileup mappability score you do not need to have 90 lines in the file. Instead you record 1 line which indicates the value for each position in that interval.

I'm wondering: why is the end of the interval the start of the next interval? Referring to your example: does position 10090 have a score of 0.000668896 or 0.000847458 ?

[Vasilisa]

Thanks, Jonathan87! This indeed makes a lot of sense!
Unfortenutely, I couldn't find any explanation neither on the UCSC website neighter in original paper by Derrien T. et al, 2012.

Regaring your question, I would say, that the position 10090 has a mappability score = 0.000847458.