Description

This track counts the overlaps of the chain links from the Self Chain alignments. It is a rough measure of how often a sequence can be found in the complete genome.

Procedure

The counting is performed:

hgsql -N -e 'select tName,tStart,tEnd from chainSelfLink;' oxyTri2 \
   > oxyTri2.chainSelfLink.bed
sort -S1G --parallel=30  -k1,1 -k2,2n oxyTri2.chainSelfLink.bed > sorted.bed
bedItemOverlapCount  oxyTri2 sorted.bed > pileUps.bedGraph
bedGraphToBigWig pileUps.bedGraph oxyTri2.chrom.sizes selfChainPileUps.bw