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aertslab / create_cisTarget_databases

Create cisTarget databases
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build mm10 regions based databases #40

Open WGLUN opened 11 months ago

WGLUN commented 11 months ago

First thank for sharing such a powerful pipeline for chromatin and motif analysis. I was trying build a mm10 database based on regions defined in ATACseq following your tutorial. However, I encounter an unexpected error. It seems it is related to motif files and annotation file. The motif files were download here: https://resources.aertslab.org/cistarget/motif_collections/v10nr_clust_public/ Could you help on how to get this resolved? Thanks

The output is like this, Traceback (most recent call last): File "/usr/local/cisTarget_databases/bin//create_cistarget_motif_databases.py", line 572, in main() File "/usr/local/cisTarget_databases/bin//create_cistarget_motif_databases.py", line 355, in main ) = get_motif_id_to_filename_and_nbr_motifs_dict( File "/usr/local/cisTarget_databases/bin/clusterbuster.py", line 102, in get_motif_id_to_filename_and_nbr_motifs_dict raise OSError( OSError: Error: Cluster-Buster motif filename "/users/working/singletons/metacluster_196.3 EcR_usp EcR/usp bergman 1.1 Hnf4a 0 None None 0.265823 FBgn0003964 D. melanogaster gene is orthologous to FBgn0003964 in D. melanogaster (identity = 26%) which is directly annotated for motif.cb" does not exist for motif metacluster_196.3 EcR_usp EcR/usp bergman 1.1 Hnf4a 0 None None 0.265823 FBgn0003964 D. melanogaster gene is orthologous to FBgn0003964 in D. melanogaster (identity = 26%) which is directly annotated for motif.

WGLUN commented 10 months ago

I figured out what happened! Please disregard or delete this topic. Thanks

jonhsussman commented 10 months ago

Hi @WGLUN, I find the same issue; would you mind describing what the solution was?

Thanks, Jonathan

WGLUN commented 10 months ago

Hi, @jonhsussman I followed this discussion here https://github.com/aertslab/create_cisTarget_databases/issues/4 to build the motif list.

ghuls commented 10 months ago

@jonhsussman You used the motif2TF file.

The motif file should contain only 1 column with the motif IDs (Cluster-Buster motif filename basename without extension):

cd v10nr_clust_public/singletons

ls -1 *.cb | sed -e 's/\.cb$//' > /tmp/v10nr_cbust_public.txt