Bioinformatics neophyte here. I'm trying to view tracks from my ChIPSeq data. I followed a fairly standard pipeline process
fastq-->align (bwa)-->bam-->sort (picard)-->call peaks (macs2)-->.broadPeak, .bdg & pileups (samtools mpileup). I also made filtered pileups for just under the peaks. My pileups have the format
<chromosome> <position> <counts>
I want to view the tracks around the peaks. I considered creating wig files from them by creating a new header each time I reach a new chromosome
variableStep chrom=<chromosome> <position> <counts> <position+1> <counts> <position+2> <counts> ... ...
I would have used
wigToBigWig to make bigWig files. But then I realized that I can just use MACS2 to spit out bedGraph files
.bdg. I did this, and they look like:
<chrom> <start> <stop> <value> KL568395.1 0 8763 0.38251 KL568395.1 8763 8833 0.55459 KL568395.1 8833 9041 0.38251 KL568395.1 9041 9111 0.55459 KL568395.1 9111 9172 0.38251 KL568395.1 9172 9198 0.55459 KL568395.1 9198 9242 1.10918 ... ...
I don't get how these are tracks of counts. Can someone please explain?