After running the three Docker steps what next??

[faizjab]

I am running pySCENIC in command line via docker. I have run the three Docker steps:

docker run -it --rm \ -v /data:/data \ aertslab/pyscenic:0.12.0 pyscenic grn \ --num_workers 6 \ -o /data/expr_mat.adjacencies.tsv \ /data/expr_mat.tsv \ /data/allTFs_hg38.txt

docker run -it --rm \ -v /data:/data \ aertslab/pyscenic:0.12.0 pyscenic ctx \ /data/expr_mat.adjacencies.tsv \ /data/hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather \ /data/hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather \ --annotations_fname /data/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \ --expression_mtx_fname /data/expr_mat.tsv \ --mode "custom_multiprocessing" \ --output /data/regulons.csv \ --num_workers 6

docker run -it --rm \ -v /data:/data \ aertslab/pyscenic:0.12.0 pyscenic aucell \ /data/expr_mat.tsv \ /data/regulons.csv \ -o /data/auc_mtx.csv \ --num_workers 6

I have now got three files: expr_mat.tsv regulons.csv auuc_mtx.csv

What do I do now? How do I complete step 8 (clustering and projection)? After that how do I create an integrated loom file for visualisation in SCope?

Any help would be greatly appreciated

[juniajvs]

Hello, what did you end up doing next? I am also trying to figure out the next steps