Aziz Khan

icon company Stanford University icon location Palo Alto, California icon location Computational biologist interested in gene regulation, machine learning, regulatory genomics and epigenomics

Results 36 comments of Aziz Khan

Differences between bedtools command line vs intervene pairwise?

Hi @unique379r are you using the same order of files (-a and -b) when computing the scores using the bedtools that you're using with the intervene?

Memory exhausted - too many files

That is a lot of BED files! The memory issue is familiar with bedtools/pybedtools using large datasets. Can you use the latest versions of bedtools and pybedtools? Also, try to...

Python 3.10 compatibility issues

Thanks for reporting this. We'll fix this in the upcoming release

Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found

I'm getting this error also, @YingYa by any chance if you fixed it.

Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found

Feel free to use this one `asntech/facets-suite:v2.0.8`. More info [here](https://hub.docker.com/r/asntech/facets-suite)

Disagreement between Intervene and BEDtools

Hi @lovelycatZ @Sarsaparella thanks for your interest and posting this. This is a known issue when doing genomic interval intersections. This is because, for genomic regions, you will not always...