Input of cisTarget databases

[Shin8a]

Hello!

I recently started using pySCENIC for my mouse snRNAseq data and have a question regarding the input requirements for the cisTarget databases used to prune indirect targets. Should I include both ranking and scores in the input, as shown below?

[mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather] [mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.scores.feather] [mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather] [mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.scores.feather]

Or is ranking alone sufficient?

[mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather] [mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather]

Since pySCENIC tutorial only use ranking but updated version of the database includes two types of dataset, I am a bit confused and would appreciate confirmation on whether my analysis is correct or not.

Thank you in advance! I'm eagerly awaiting my results!

[ghuls]

You only need *.genes_vs_motifs.rankings.feather.

[Shin8a]

Thank you for your reply! Very appreciated! I will try it later:)

[ctlshcxy]

You only need *.genes_vs_motifs.rankings.feather.

Hi, I'm also confused about this question, could you please explain when to use scores.feather file?