pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
I got thousands of these warnings when I run pyscenic ctx on linux (ubuntu 22.04) CLI (conda environment):
pyscenic.transform - WARNING - Less than 80% of the genes in some_gene could be mapped to hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather. Skipping this module.
or
pyscenic.transform - WARNING - Less than 80% of the genes in Regulon for some_regulon could be mapped to hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather. Skipping this module.
I used the [mc_v10_clust] database and motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl, adjacency matrix from pyscenic grn command was created successfull.
hanjun98
commented
8 months ago
I got thousands of these warnings when I run pyscenic ctx on linux (ubuntu 22.04) CLI (conda environment):
pyscenic.transform - WARNING - Less than 80% of the genes in some_gene could be mapped to hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather. Skipping this module.or
pyscenic.transform - WARNING - Less than 80% of the genes in Regulon for some_regulon could be mapped to hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather. Skipping this module.I used the [mc_v10_clust] database and motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl, adjacency matrix from pyscenic grn command was created successfull.
My output file is empty. What I do wrong?