Alexander Lenail

@dpryan79 what is the fastest way to get arrays of values from a bigwig file for each of many genomic intervals (i.e. entries in a bed file)?

Did anyone ever get to this?

Sorry I may have been misreading the error message. The important bit might just be ``` Error in py_call_impl(callable, dots$args, dots$keywords): anndata._io.utils.AnnDataReadError: Above error raised while reading key '/layers' of...

in python, I can do ``` import anndata adata = anndata.read_h5ad(input_file) ``` without any issues. The `input_file` was created with `scanpy.write_h5ad()` -- scanpy version '1.9.1', anndata version 0.8.0. The file...

@lazappi yes! It was just a version issue

@wheaton5 what if there are more sample IDs in the input than clusters? E.g. what if my 10x run contains cells from 10 out of the 100 patients in my...

Thanks @wheaton5. How does one relate the souporcell cluster_genotypes.vcf samples (clusters) with samples in a VCF from genotyping? Would very much appreciate your recommendation -- and I think others would...

Thanks @wheaton5. Do you know of a better tool than [GenotypeConcordance (Picard)](https://gatk.broadinstitute.org/hc/en-us/articles/360037051292-GenotypeConcordance-Picard-) to accomplish that?

I'd like to note I'd also love to see a recommended way to relate known genotypes to SoupOrCell output clusters post-hoc (some option to do `--known_genotypes` after having already run...

I too would like this. I'd like to interleave left-justified `\text{explanations}` among `\begin{aligned} equations`. What I have now: