Gökçen Eraslan

Hey @davidsebfischer, yeah I mean, not that I'm super interested in p-values around 10^-180, but it's just a technical error to have relatively low granularity in p-values, which ideally shouldn't...

I think a vectorized version of bw.values would be much better e.g. `bw.values(np.array([chrom]*3), np.array([79250, 86700, 87277]), np.array([80250, 87700, 88277]), numpy=True)` which returns a list of numpy arrays, without iterating over...

> Oh, and I'd suggest adding suffixes to existing model names like `_counts` to indicate you're taking sufficient stats rather than the raw data. You mean adding `_counts` to the...

I also get this error sometimes, no clue.

I can reproduce this only with the full dataset which is already very big, I'll try to reproduce it with a subset and let you know. Thanks.

Hi Haynes, Thanks a lot for the quick reply! I see. Actually, given that I am no expert of any aligners, I would love to give HISAT2 a try and...

Oh I didn't know about the `--aligner` option in souporcell-pipeline.py (https://github.com/wheaton5/souporcell/blob/master/souporcell_pipeline.py#L31) at all. Btw, I'm not using the singularity build at all, I'm using a custom docker image (available at...

Thanks for everything. So the final questions: - Do you think it makes a big difference to use the "genome_snp_tran" HISAT2 index compared to the "genome_tran"? - I see that...

OK thanks. I was just considering existing hisat2 index files.

The filenames of the existing index files are `grch38/genome.1.ht2`, `grch38/genome.2.ht2` etc., the `-x` parameter should be `grch38/genome`.