Thouis (Ray) Jones

It looks like it's using an existing .bedgraph file instead of recalculating. Could you remove *.bedgraph in the Neighborhoods subdirectory and re-run with the pysam branch?

That's very strange. Could you add a line to https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/master/src/predictor.py#L191 just before the merge printing out summ1.head() and summ2.head()? I can't see how these would have non-overlapping indices. It looks...

Which branch is the docker running?

Can it be moved to the use_pysam branch?

@engreitz - do we have these?

@jnasser3 - Can you answer this?

Looks like the chromosome sizes have mixed space-and-tabs. I think changing your awk command to this will fix it: `awk -v OFS='\t' '$1 = $1 OFS "0"' ./reference/hg38.chrom.sizes > ./reference/hg38.chrom.sizes.bed`

Could you try checking out the `use_pysam` branch and see if that fixes this problem? It did in my copy of your script and data. You'll need to pip install...

Could you change allow_vc to False in the header of this function and see if that helps? https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/b6f23f3118216d721bd4abb19fec21e6fa38fdd5/src/hic.py#L6 If so, maybe we can make the logic in this function less...

I think without HiC, you'll need to switch it to use powerlaw.Score via `--score_column powerlaw.Score`