Caleb Lareau

@Funshope You need the correct version of gfortran installed; see here: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/

@Funshope you're super close! I think that the Cpp code is compiling now; there's a pesky dependency (`GO.db`) that doesn't automatically install (https://github.com/GreenleafLab/chromVAR/issues/17 ) Try this in `R`: ``` source("https://bioconductor.org/biocLite.R")...

Here's my attempt at modifying this script from @AliciaSchep -- https://github.com/GreenleafLab/chromVAR/blob/master/R/motifs.R ``` getJasparMotifs2018

Here's my attempt at it as well-- https://github.com/caleblareau/scATAC_10X_raw_to_kmers/blob/master/example_kmers.R

@AliciaSchep the "fragments.tsv.gz" file that is the basis of the fragments is the same. The additional file that I reference is essentially the barcodes that pass filter based on 10X's...

I think that it's relatively easy to do a post-hoc filtering from the standard getCounts, so I wouldn't worry too much about it in general (unless you are feeling over-ambitious)....

I would say that it's technically right in that the variability is a measure that can be applied to two samples. However, you probably almost certainly have some technical confounder...

Bumping that this would be extremely useful for me in computational biology / genomics research as well.

Hm strange... it's erroring out at not finding a 'depth' file per barcode; can you see if this command works? ``` mgatk bcall -i barcode/test_barcode.bam -n bc1_tenx -o tenx_test -bt...

I'm getting the same error... was this ever addressed or does a workaround exist?