Thouis (Ray) Jones

I was confused. However, it's not clear from the docs the difference between the structuring element neighborhood and structuring element value. Is the SE neighborhood all nonzero entries, or are...

Ok. This was partly me not understanding the generalization of binary erosion to grayscale, having only used it with 0-height structuring elements. You might document that as well, for confused...

@engreitz @jnasser3 - can you address the whitelist questions? For 3, yes, replicates are almost always better.

@jnasser3 - do you have an answer for this?

I think your /apps/a/chr may be in DOS format (\r instead of \n for line endings), based on 248956422 being the length of chromosome 1.

Could you try these two things (together): - remove any files in /apps/j/output-neighborhoods29/ - check out the `use_pysam` branch of the repository to see if it fixes the memory error.

Sorry, should have been clearer. You'll need to sort each bam by position and run samtools index on it. On Sat, Sep 26, 2020, 21:46 londonlondon20 wrote: > Okay. used...

Yes. I'd suggest using the sc-ATAC to create pseudobulk (with or without evening out reads per-cell) ATAC, and it should work similarly to using bulk ATAC.

I wonder if this is an error in the precalculated files. Could you check the contents of …/Neighborhoods/Enhancers.H3K27ac*? How many lines does it have, vs how many are there in...

I've just added a branch `use_pysam` that you might check out and see if it addresses this crash. I'll also look into putting the code into a docker container.