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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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pyscenic ctx AssertionError: Found 2018 genes present but missing from the expression matrix #513

Closed LacquerHed closed 12 months ago

LacquerHed commented 12 months ago

pyscenic ctx found more genes present via adj than expression matrix while the same loom file was used as input to both the grn and ctx commands, and maybe Im missing something but that file should only contain a single expression matrix of all genes or are the two commands pulling separate matrices? Thanks.

Commands for both:

arboreto_with_multiprocessing.py \
    /gpfs/projects/pySCENIC/SeuratLoom.loom \
    /gpfs/projects/pySCENIC/allTFs_mm.txt \
    --method grnboost2 \
    --output /gpfs/projects/pySCENIC/adj.tsv \
    --num_workers 40 \
    --seed 777
pyscenic ctx /gpfs/projects/MallipattuGroup/Rob/pySCENIC/adj.csv /gpfs/projects/pySCENIC/cistarget_database_mouse/*feather --annotations_fname /gpfs/projects/pySCENIC/motif2tf_mouse/motifs-v10nr_clust-nr.mgi-m0.001-o0.0.tbl --expression_mtx_fname /gpfs/projects/pySCENIC/SeuratLoom.loom --output reg.csv --mask_dropouts --num_workers 40`

pySCENIC 0.12.1 CLI on HPC via Slurm CentOS