## 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