how to plot a TSS profile using an external quantification for Watson and Crick strand

Question

[Lila M]

Hi everybody, I have an issue here, let's say I have this kind of data:

     chr    w_start  w_end  ratio_w  ratio_c chr txt_start txt_end  strand   gene
    chr1    879000  879999  0.102   0.306   chr1    879584  882440  -   ENSG00000188976
    chr1    879000  879999  0.102   0.306   chr1    879584  894670  -   ENSG00000188976
    chr1    879000  879999  0.102   0.306   chr1    879585  893838  -   ENSG00000188976
    chr1    880000  880999  0.357   0.102   chr1    879584  882440  -   ENSG00000188976
    chr1    880000  880999  0.357   0.102   chr1    880699  880942  -   ENSG00000188976
    chr1    880000  880999  0.357   0.102   chr1    879584  894670  -   ENSG00000188976
    chr1    880000  880999  0.357   0.102   chr1    879585  893838  -   ENSG00000188976 
    chr1    881000  881999  0.153   0.051   chr1    879584  882440  -   ENSG00000188976

where w_start w_end is window start and end, ratio_w ratio_c is ratio in Watson and Crick strand and the other part of the data refers to transcription factors of interest. I would like to plot the typical TSS profile using the ratios for Watson and Crick strand around my TSS (something like the figure1e of this paper. But I can't figure out how to do it in R. Any suggestions?

[ATpoint]

Hi Lila M , please have a look at either the deeptools documentation if you want something via command line or e.g. the genomation package in R. Both can do it, documentation is extensive.

[Lila M]

Thank you for the tip, but as far as I understand, deeptools needs the bam files or bigwig files (I only have this bed file to work with). I will have a look into genomation as I never work with it before.

[Lila M]

Sorry but I can't figure out how to do it with those programs, more help will be very handy! Thanks!