search

Taiji-pipeline / Taiji

All-in-one analysis pipeline
https://taiji-pipeline.github.io/
BSD 3-Clause "New" or "Revised" License
33 stars 9 forks source link

Score in GeneRanks.tsv #34

Open Xieeeee opened 1 year ago

Xieeeee commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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