bed files for deeptools

Question

[kanwarjag]

I am interested in generating figs from http://www.ncbi.nlm.nih.gov/pubmed/22431625

Especially figs 2- A,D, F H related to Chipseq. I am using mm9. As suggested I can use deep tools. I have to run Compute matrix with my bam file to generate heatmapper compatible bigWig file. However my question is which bed file has to be used to generate plot across TSS or genebody as well as combined in Compute matrix. Is there any online source of such files.

Thanks

Answer 1

[Alternative]

You can get TSS and gene infomration from UCSC. Check "computMatrix" parameters to plot either scaled or per bp position information.

Use deepTools-1.6 (branch version) from github if you want to have different plots on the same graph.