Saeed

Hi, indeed, you have to binarize your auc matrix for automatic thresholding. You may try ``` from pyscenic.binarization import binarize binarized = binarize(auc_mtx, num_workers = 22) binarized.to_csv("binarized_mtx.csv") ```

> Hi @MaybeJustJames , > > Thanks for the suggestion. pySCENIC does actually have process tracking built in for a number of steps, although it's maybe not always obvious. >...

Thank you @cflerin . I shall try the multiprocessing script and maybe the dask scheduler as well. Thanks and Kind Regards, Saeed

Hi, `wget https://raw.githubusercontent.com/aertslab/pySCENIC/master/scripts/arboreto_with_multiprocessing.py ` I see that this script is no more available at scripts folder.

Had same problem. Solved this way. Ran samtools first to get the cellsorted_possorted.genome_bam.bam file. And then ran velocyto. In the velocyto documentation, it says "If the file cellsorted_[ORIGINALBAMNAME] exists, the...

Hi, Thanks for discussing this issue. I am running into issue of `FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'` So I tried, `$pip install pysam` `Requirement already...

I installed samtools. However it still comes back with same error. Can someone advice, where I should place the samtools directory for it to be read properly by velocyto? ```...

Hi, @igordot Thanks for the suggestion. Indeed, installing samtools with conda worked. I am now hitting another strange error. I am allocating 10 threads with 24 gb each for the...

Solved. Ran samtools first to get the cellsorted file. And then ran velocyto in the documentation, it says "If the file cellsorted_[ORIGINALBAMNAME] exists, the sorting procedure will be skipped and...

I am using 240 GB for a 1000 cells and still hitting the same error. No idea what is going wrong. Samtools is version 1.9 `~$ velocyto run10x -m /alltracks_mask.gtf...