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.
If you understand R code, this is my code for doing exactly what you want. I wrote this a while ago so my code is awful but you might be able to pull out some useful stuff! http://rpubs.com/achitsaz/94710
I have written R script which can probably solve your problem. For given set of genes in bed format, it will give you averaged line plot or even you can generate heatmap for each gene. Script needs two files
1) set of genes in bed format
2) alignement data in .bedgraph format.