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A signal track is a bedGraph (BED3+) file with an entry for every base in a defined set of regions that shows the count of overlapping bases for the regions (see https://genome.ucsc.edu/goldenpath/help/bedgraph.html). bedGraph files can be visualized in the Broad's IGV (Integrative Genomics Viewer) application (https://software.broadinstitute.org/software/igv/download) or in the UCSC Genome Browser (https://genome.ucsc.edu/).

• Go to the UCSC Genome Browser: https://genome.ucsc.edu/
• Select Genomes from the top menu bar
• Select Human from POPULAR SPECIES
  • under Human Assembly select Feb 2009 (GrCh37/hg19)
  • select GO
• In the hg19 browser page, the Layered H3K27Ac track is a signal track
  • the x-axis is the genome position
  • the y-axis represents the count of ChIP-seq reads that overlap each position
    • where the ChIP'd protein is H3K27AC (histone H3, acetylated on the Lysine at amino acid position 27)

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Because this bedGraph file is for the small-ish (12Mb) yeast genome, and for reads that cover only part of that genome, it is not too big – only ~34M. But depending on the species and read depth, bedGraph files can get very large, so there is a coresponding corresponding binary format called bigWig (see https://genome.ucsc.edu/goldenpath/help/bigWig.html). The program to covert a bedGraph file to bigWig format is part of the UCSC Tools suite of programs. Look for it with module spider, and note that you can get information about all the tools in it using module spider with a specific container version:

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Looking at the help for bedGraphToBigWig, we'll need a file of chromosome sizes. We can create one from our BAM header, using a Perl substitution script, which I prefer to sed(see Tips and tricks#perlpatternsubstitution):

module load ucsc_tools

cd $SCRATCH/core_ngs/bedtools_genomecov
bedGraphToBigWig  # look at its usage

# create the needed chromosome sizes file from our BAM header
module load samtools
samtools view -H yeast_mrna.sort.filt.bam | grep -P 'SN[:]' | \
  perl -pe 's/.*SN[:]//' | perl -pe 's/LN[:]//' > sc_chrom_sizes.txt

cat sc_chrom_sizes.txt

# displays:
chrI    230218
chrII   813184
chrIII  316620
chrIV   1531933
chrV    576874
chrVI   270161
chrVII  1090940
chrVIII 562643
chrIX   439888
chrX    745751
chrXI   666816
chrXII  1078177
chrXIII 924431
chrXIV  784333
chrXV   1091291
chrXVI  948066
chrM    85779

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cd $SCRATCH/core_ngs/bedtools_genomecov
export LC_COLLATE=C  # may or may not need this...
sort -k1,1 -k2,2n yeast_mrna.genomecov.bedGraph > yeast_mrna.genomecov.sorted.bedGraph
bedGraphToBigWig yeast_mrna.genomecov.sorted.bedGraph sc_chrom_sizes.txt yeast_mrna.genomecov.bw

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