create_cisTarget_databases
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aertslab
Create cisTarget databases
Hi I managed to run create_cistarget_motif_databases.py for zebrafish and it generated three . feather files, `zf.genes_vs_motifs.rankings.feather`, `zf.genes_vs_motifs.scores.feather` and `zf.motifs_vs_genes.scores.feather`. How can I run `create_cross_species_motifs_rankings_db.py` ? because `create_cistarget_motif_databases.py` output did not...
Thank you for developing this amazing tool! I am wondering if zebrafish cisTarget databases will be available in the future, like for human/mouse/drosophila?
Hi, Regarding the @tropfenameimer comment on the build of Gallus gallus cisTarget database issue #4, I tried to take similar steps for building pig cisTarget database. First, I got the...
Hi team, Thank you for the nice explanation about database building. I want to create a database for zebrafish using "create_cistarget_motif_databases.py". I am struggling to get a zebrafish genome region...
First off, thanks for putting this together for the community. I am trying to create a cisTarget track DB for mouse to use with pySCENIC, using a number of ChIP-seq...
Is there a possibility of adding example data for running these scripts?
Hi, can the input motifs be in the PWM format? Like outputs from HOMER program (motif1.motif), an example please check bellow: ```bash >TGCATG 1-TGCATG,BestGuess:hsa-miR-4262 MIMAT0016894 Homo sapiens miR-4262 Targets (miRBase)(0.647)...
@honghh2018 You can use the mouse or human motif table and replace the gene_name column with the homologous gene for rat. You can get them for example with Ensembl biomart:...
Hi, Maybe I'm getting this totally wrong, but from the README file it seems that to annotate regulatory regions for each gene or region, you can either use a motif...
