Gert Hulselmans

Conversion to HOMER format with Log odds detection threshold is difficult. As far as I know, it would only be possible if you have access to the original sequences (positive...

use the `test.genes_vs_motifs.rankings.feather`. Did you add this option when creating the gene database (it will strip of `#some_number` from the region names in your fasta file and should match the...

Start in a new dir (or move/delete the current feather files) and create a gene rankings database: ```python fasta_filename= motifs_dir= motifs_list_filename= db_prefix= nbr_threads=22 # Create gene rankings database. "${create_cistarget_databases_dir}/create_cistarget_motif_databases.py" \...

as long as the "gene" names match in the rankings database and the expression matrix, it should work.

You can only use `test.genes_vs_motifs.rankings.feather`. All other feather files can be deleted, they are needed to create `test.genes_vs_motifs.rankings.feather`. - `test.motifs_vs_genes.scores.feather`: Cluster-Buster creates scores for regions/genes in your FASTA file per...

Instead of `test.genes_vs_regions.rankings.feather`, it should have been `test.genes_vs_motifs.rankings.feather`, my bad.

How does your signatures file look like?

You can use: ```python # cd create_cisTarget_Databases import feather_v1_or_v2 all_columns_in_ctx_db = get_all_column_names_from_feather(feather_file="hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather') all_columns_in_ctx_db ``` Gene names for hg38 are HGNC symbols as linked to RefSeq r80.

You don't need to compile Cluster-Buster to be able to check the feather databases. You just need to create a conda environment with the python dependencies and then when you...

Creating databases for species we don't use in the lab, probably needs to be a community effort as validating that the input regions used to create the database work properly...