Me and a ex lab member generated two heatmaps using the same Pol II dataset using HOMER and deeptools.
I used deeptools, and the ex lab member used HOMER. The heatmaps look 'very' different, though their patterns are similar. My PI however seems to think that because of this, my heatmap is un-reliable so i'm here hoping that someone could shed some light on the discrepancies.
HOMER heatmap was generated using protocol from this site: http://homer.salk.edu/homer/chipseq/heatmap.html
annotatePeaks.pl refseqTSS.bed hg19 -gtf reference_data.gtf -size 10000 -hist 50 -ghist -bedGraph bedgraphfiles.bdg
Deeptools heatmap was generated using the following
computeMatrix reference-point -S /Users/Carlos/Dropbox/ChIP-Seq/hg19/old_data/Sample_Pol-II-Chip-N20/Tracks/Pol-II-Chip.normalized.bigWig -R /Users/Carlos/Desktop/Projects/GenomicDataPublication_Project/Gencode/genes_proteincoding_gencodev19.bed -a 5000 -b 5000 -out computeMatrix_pol --referencePoint TSS --averageTypeBins max --missingDataAsZero --skipZeros --numberOfProcessors "max" -bs 50 plotHeatmap -m /Users/Carlos/Desktop/Projects/GenomicDataPublication_Project/Gencode/computeMatrix_pol -out pol_heatmap2.pdf --sortUsing mean --averageTypeSummaryPlot mean --colorList white black --heatmapHeight 15 --samplesLabel "Pol II" --legendLocation none --heatmapWidth 3
The images generated: