Is TSS enrichment plot showing the correct output?

[kkupkova]

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Hi! I have deeptools 3.3.1 / Python 3.7.3 and I am not reporting an error, rather concern. I have been struggling to replicate the results from --referencePoint TSS when I generate my custom list of TSSs (just 1 bp) and run computeMatrix reference-point with a, b set to 2000. I was able to replicate the results when I generated a new list of TSSs, where I didn't take into account the strand. Shouldn't a TSS of a gene on "-" strand be in fact its end coordinate?

[dpryan79]

Yes, the strand is taken into account, so please double check that when you manually generated 1-base BED file that you did in fact get the correct coordinates. You can also check the signals reported by gunzipping the output and having a look (it's just a text file).