Gert Hulselmans

Does any of the following commands print any output (lines with only ">") ? ``` grep '^>$' "updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa" grep '^>$' "Numbered_updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa" ``` Does samtools complain when you try to make...

In the original FASTA file there are a lot of genes which have "Sequence unavailable" ``` # Number of "sequences" $ grep -c '^>' updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa 57263 # Number of "sequences"...

You can use a BED file with pseudobulk peaks from your scATAC data and use bedtools to make the FASTA file: ``` bedtools getfasta \ -fi Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa \ -bed pseudobulk_peaks_from_scATAC.bed...

zsync files are removed for now as zsync was having issues with big files (larger than 2G) for a long time. Looks like the zsync2 bug: https://github.com/AppImageCommunity/zsync2/issues/31 might finally be...

Yes for now the README is focused on motifs. For tracks the script still needs to be written but conceptually it is quite similar to https://github.com/aertslab/create_cisTarget_databases/blob/master/create_cistarget_motif_databases.py, but instead of using...

yes you can, but you need to make sure you have a lot of ChIPseq tracks in your database as else they will always be enriched in each analysis. For...

@mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py` https://github.com/aertslab/create_cisTarget_databases#create_cistarget_track_databasespy

SCENIC is designed for doing motif enrichment of proteins that bind to DNA (transcription factors), so using it for RBPs probably does not make much sense.

You will need to change at least the the first step of pySCENIC (gene regulatory network) with something that makes sens for RBPs. Probably you are aware, but if not,...

If you know which RBPs bind to which targets, you won't need the GRN related code of pySCENIC as there the TF to target gene relation is inferred and not...