Score in GeneRanks.tsv

[Xieeeee]

Hi Kai,
I am using Taiji to Paired-Tag data. A naive question, what's the score in the GeneRanks.tsv file generated? Is it the PageRank score after filtering out non-significant TFs? I didn't find the GeneRanks.html file in the directory and I wonder whether I can use the score or the p-value for plotting a heatmap as you show in the tutorial

Thanks so much!

Best,
Yang

[kaizhang]

Hi Yang, the scores in GeneRanks.tsv are pagerank scores (TFs' global importance) described in https://www.science.org/doi/10.1126/sciadv.aav3262. They sum up to 1. The HTML file uses some predefined cutoffs to generate the visualization. If there is no TF passing the cutoff then no visualization is generated.

For single-cell data, you can use SnapATAC2 to perform a similar (more sophisticated) analysis, I haven't written the tutorial for this though. Let me know if you want to try it.

[Xieeeee]

Hi Kai,
Thanks for the quick response. I asked because in my result the scores don't add up to 1. It would be really nice if you can help me look into this.

The result can be found on silencer: /projects/ps-renlab/y2xie/projects/scifi-multiome/14.mESC_Multiome_PT/taiji/GeneRanks.tsv

[kaizhang]

The GeneRank.tsv contains only TFs but not all genes. So the sum is less than 1.