04 May 2010

Mapability vs Sequencing Depth

I'm currently trying to see if there is be a correlation between the MAPABILITY and the SEQUENCING DEPTH.

The MAPABILITY, generated for the ENCODE project , is the level of sequence uniqueness of the reference hg18 genome. Scores are normalized to between 0 and 1 with 1 representing a completely unique sequence and 0 representing the sequence occurs >4 times in the genome. A score of 0.5 indicates the sequence occurs exactly twice, likewise 0.33 for three times and 0.25 for four times.

The Sequencing depth represents the (often average) number of nucleotides contributing to a portion of a NGS assembly. On a genome basis, it means that, on average, each base has been sequenced a certain number of times

I've been trying to plot the relation between the mapability*100.0 (X-Axis) and the Sequencing depth( log(Y-Axis),cut-off:100 ) for my data on the human chr1 . The radius of the circles is proportional to the number of times a pair(mapability/depth) was found.
Hum... as far as I can see, nothing really obvious is visible here, but on the other hand, I'm not sure I used the best visualization...

(BTW the image below was created using a base64 endcoding src="data:image/png;base64,iVBORw0KG...". I hope it will be displayed within blogger.com)


That's it


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