I recently work on several ChIP-seq data sets. My traditional workflow is .fastq/.fastq.gz -> .sam (via Bowtie) -> MACS (after BAM conversion) -> wig to bigwig conversion. Thus, my usual output are .bw track files that I then view through UCSC genome browser, with the y axis (track height) scaled to sequencing depth (for example the Bowtie alignment reported 15M aligned reads, y axis would be 1 - 15).
However, recently I encountered an issue with MACS, or more precisely, wigToBigWig tool:
Overlap on chr4 between items starting at 29999999 and 30000000. Please remove overlaps and try again Fatal error: Matched on Error Error running wigToBigWig.
I followed the suggestion of the Galaxy team and tested out MACS 2 and succeeded constructing a BedGraph file, which I then converted to .bw track to view through UCSC genome browser as usual. The result was very good. However, I noticed that the y-axis scaling is different from what I usually have with MACS -> bigwig method. In MACS2 -> bigwig case the peaks are only visible with y-axis range being 0.4 - 0.6, while in traditional MACS -> bigwig case peaks are usually visible with the range being 1 - 15 (as I mentioned above). Is there a way to change the scaling of the track created by MACS2 -> bigwig method to match the scaling scheme that I usually use for with MACS -> bigwig?
Here is the link to the history in question: https://usegalaxy.org/u/sushivision/h/tks367b3-0113
I must admit that my understanding of ChIP-seq analysis is very shallow. Please feel free to critique my practices. I would greatly appreciate an explanation for the meaning of track height if anyone can provide it.