Generate heatmap files from BigWig data.
In order to run the plotting script, you need a config "instruction" file. The file should look like the following template:
Bed/Wig/pdf filename min max step colormap title description
My config.txt contains the following:
bed hg19/tata_plus.bed 50 50 TATA-Plus
bed hg19/tata_minus.bed 50 50 TATA-Minus
bw hg19.100way.phyloP100way.bw -4 4.02 2 BuRd PhyloP Conservation Score
bw hg19.100way.phastCons.bw 0 1.02 0.5 Reds PhastCons Element Conservation
bw ENCFF000SLA.bigWig 0 50.2 25 Hot K562 Base Overlap Signal
bw ENCFF000SPQ.bigWig 0 20.2 10 Hot HeLa Base Overlap Signal
bw GSM1480321_K562_GROcap_wTAP_plus.bigWig 0 10.2 5 Reds Plus Read
bw GSM1480321_K562_GROcap_wTAP_minus.bigWig -10 0.5 5 Blues Minus Read
pdf tata_profile.png size
Then run the following command:
main.py config.txt
If this software was helpful please consider citing it with:
Mahpour A, Scruggs BS, Smiraglia D, Ouchi T, Gelman IH (2018) A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters. PLOS ONE 13(10): e0205608. https://doi.org/10.1371/journal.pone.0205608