Hi I am trying to compare the effects of 2 transcription factors. I have the initial data files in .bed format on which I used MACS to get output .bed files again for peak calling.
My genome does not have a specific GTF file and it is not fully annotated so I only have a GFF3 file. AnnotatePeaks.pl of HOMER worked well and I have the TSS binding sites of genes isolated.
My question is
I want to plot a line plot from -1000 to +500 relative to the ATG region of each binding sequence to show the average binding signal over all genes for both the transcription factors. Most of the programs I saw use GTF files which I do not have!
Also is there is a way to combine both the transcription factor peaks together on a single plot? I couldnt really find a tutorial that puts the TSS at ATG at position 0 and makes a graph.