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Mapability index (track) from UCSC

Hi,

I used the UCSC Mapability track to calculcate the mappability of my regions of interest. So, I used the following settings:

clade: Mammal
genome: Human
assembly: hg19
group: Mapping and Sequencing Tracks
track: Mapability
table: wgEncodeCrgMapabilityAlign100mer

I chose the 'defined regions' and then input my region in bed format.

The output added 1 column at the end of each line that added something like the following:

chr1.1

What does this mean? Does the '1' in the end mean that it only maps to one region? What if it maps to 2 or more, what will it say then?

Thanks!

~N

ucsc mapability
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updated by Ram Ram • written by Floydian_slip Floydian_slip

1 answer

I tried the above configurations, and agree that the result looks not easy to comprehend.

However, changing the output format to 'data points' yields reasonable results:

Example:

track type=wiggle_0 name="CRG Align 100" description="Alignability of 100mers by GEM from ENCODE/CRG(Guigo)"
#bedGraph section chr21:32976481-33136142
chr21   33029853    33033699    1
chr21   33033699    33033700    0.5
chr21   33033700    33033701    0.166667
chr21   33033701    33033702    0.125

meaning that in the first line, the 100mer mapped to one unique spot in the genome. The second line to 2 spots, the third line to 6 spots, the fourth line to 8 spots and so forth.

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updated by Ram Ram • written by Noushin N Noushin N

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