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wheaton5 / souporcell

Clustering scRNAseq by genotypes
MIT License
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Not clustering samples #87

Open ManuCrick opened 3 years ago

ManuCrick commented 3 years ago

Dear all, I'm trying to use Souporcell to divide five 10X samples from various patients. It apparently runs fine but the clusters.tsv file is only returning cluster 0 for all the barcodes. I thought it was a problem with my data so I decided to run the practice/testing data set and obtained a similar clusters.tsv file with all the barcodes as cluster 0 and not what is shown in the tutorial (0 and 1). I am running Souporell on my institute cluster with the command:

singularity exec -B /path/to/my/data/Souporcell/test/:/dummy_path souporcell.sif souporcell_pipeline.py -i /dummy_path/A.merged.bam -b /dummy_path/GSM2560245_barcodes.tsv -f /dummy_path/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa -t 8 -o /dummy_path/soup_outs/ -k 1

Thanks for all the help!

Zethson commented 3 years ago

You must increase your k. k is the number of clusters.