Motifs not present

[francicco]

Hi,

I'm very new to this. So apologies if I say/do something incorrectly. From my understanding, in order to run SCENIC analysis on my non-model insect species (a butterfly), I need a motif database that I have to create with create_cistarget_motif_databases.py. What I did so far was to:

1. Download the table of motifs for Drosophila, motifs-v10-nr.flybase-m0.00001-o0.0.tbl or motifs-v9-nr.flybase-m0.001-o0.0.tbl, not sure which one to use. Done
2. Get the orthologous genes with my species (I'm guessing single-copy might be a good start). Done
3. Get the associated motifs from motifs-v10-nr.flybase-m0.00001-o0.0.tbl or motifs-v9-nr.flybase-m0.001-o0.0.tbl. Done.
4. Download the singletons cb files. Done
5. Execute create_cistarget_motif_databases.py:

python create_cistarget_motif_databases.py -f assembly.fasta --motifs_dir v10nr_clust_public/singletons --motifs MyMotifs.txt --output MyTFmotifs

When I do that it says that "bergman__Abd-B.cb" does not exist for motif bergman__Abd-B, and in fact it's not there.

I guess one question would be where do I get all the cb files, and am I doing right so far?

Thanks a lof
Francesco

[francicco]

I think I sorted it. Now I'm running pyscenic.
Thanks anyways
Cheers
F