Description

This track is a graph of the density of the chain alignments from Cow bosTau4. There are some unusual pile-ups between these two genomes.

Methods

A bed file of the chains was made:

$$ zcat susScr2.bosTau4.all.chain.gz | grep "^chain " \
        | awk '{printf "%s\\t%d\\t%d\\t%s\\t%s\\t%s\\n", $$3, $$6, $$7, $$8, $$2, $$5}' \
        > bosTau4.chain.bed

The chain scores were scanned with ave, to find the range of scores:

  ave -col=5 bosTau4.chain.bed
Q1 5300.000000
median 8265.000000
Q3 14079.000000
average 12729.401671
min 3000.000000
max 1506828099.000000
count 144157201
total 1835034915327.000000
standard deviation 419128.061072

The bed file scores were normalized to the range 0-1000 and an overlap count bedGraph file was calculated, and turned into a bigWig:

$$  awk '
  {printf "%s\\t%d\\t%d\\t%s\\t%d\\t%s\\n", $$1,$$2,$$3,$$4,(1000*$$5)/1506828099, $$6}' \
        bosTau4.chain.bed | sort -k1,1 -k2,2n > bosTau4.chain.normalized.bed
$$  bedItemOverlapCount susScr2 bosTau4.chain.normalized.bed \
    > bosTau4.overlap.wigVar
$$  bedGraphToBigWig bosTau4.overlap.wigVar susScr2.chrom.sizes bosTau4ChainPileUp.bw
$$  bigWigInfo bosTau4ChainPileUp.bw
version: 3
isCompressed: yes
isSwapped: 0
primaryDataSize: 188,237,695
primaryIndexSize: 1,267,372
zoomLevels: 10
chromCount: 20
basesCovered: 2,255,615,700
mean: 28.797958
min: 1.000000
max: 14674.000000
std: 202.526527