rauldiul

splitBam fragment sizes for nucleosome-free DNA

2

Hi, I'm using your package and have a general question regarding the sizes in which BAM file is split with splitBam to generate nucleosome-free, mononucleosome... fragments. I see that the...

RunAzimuth ATAC working for BMMC but not for PBMC atlas

4

Hi! Thanks for your great software. I'm using Azimuth locally, with `RunAzimuthATAC` and having downloaded the PBMC and the BMMC reference `ext.Rds` objects from the Zenodos (https://zenodo.org/record/7770374, https://zenodo.org/records/7770389). Using these...

Are output coordinates one or zero-based?

3

Hi! Thank you for your work!! I have a simple question: the epic2 output comes in BED-similar format, however, I'm not sure if the output is really 0-based. When I...

Hi, thanks for your invaluable software and resources. I'm handling some EPICv2 data and I accessed your annotations to genes located here: https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/EPICv2/EPICv2.hg38.manifest.gencode.v41.tsv.gz This matrix has a `probe_strand` variable. I...