Mary O'Neill

I got the same error when I tried to run demuxlet with a VCF of 14 individuals (5726916 variants, 515M) and my 10X data, even when requesting up to 40Gb...

@wheaton5 @cotedivoir @arutik @ktpolanski I realize this is an old thread, but it is very relevant to what I am hoping to accomplish and I would love your feedback if...

Thanks @wheaton5! It is not clear to me where to find the 'total log likelihood' plotted in figure 2. Would I obtain this by running souporcell with various k parameters...

I do not see any out files, sorry!

I am guessing it is this: ==> clusters.err

> I've mostly used the elbow plot method showed in the paper figure 2. But this is much less effective when there is a very skewed cluster sizes because the...

@wheaton5 I'd love to beta test it on some problematic data I have. Will it work if there is more than 2 individuals? I'm mostly just after cleaning a dataset...

No, it is a non-commercial single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) method: https://www.nature.com/articles/s41596-022-00752-0

Thanks Haynes! I'll modify the bams, select for cells, and give it a try.