Gert Hulselmans

Seems it should be possible with `-C` option and adding the info of the barcode read as a comment.

The file needs to be named: `mm9-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather` (the last part of the filename needs to end with `genes_vs_motifs.rankings.feather`. The databases can be found now on the resources webserver: https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather The...

Databases in Feather v2 format can be navigated at: https://resources.aertslab.org/cistarget/databases/

pySCENIC v0.12.0 is out: https://pypi.org/project/pyscenic/. https://resources.aertslab.org/cistarget/databases/ is updated too.

Mayb try to set `--num_workers 20` to a lower value. It could be that you are running out of filedescriptors. You can see the current limits with: ```bash # Open...

@cflerin Can you post `head $MOTIF_ANNOTATIONS_FNAME`?

This is not a motif2tf file. but a track to TF file.

Can you convert your file with the following command? ``` awk -F '\t' -v 'OFS=\t' ' { if (NR == 1) { print "#motif_id", "gene_name", "motif_similarity_qvalue", "orthologous_identity", "description"; } print...

Do your gene names match any of the TFs listed in the motif annotation filename, else no genes will be selected. Also for `mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather` the matching motif annotation filename is...

What is the output of: ``` curl -v -O -L -R https://resources.aertslab.org/cistarget/motif2tf/motifs-v9-nr.hgnc-m0.001-o0.0.tbl ```