getValidBarcodes() need to be modified to compatible with the output of Cell Ranger ATAC version higher than 2.0

[cherrie-g]

Describe the bug Hi there, I‘m using ArchR to analysis my ATAC data. And I want to do barcode filtering in createArrowFiles step. I found that getValidBarcodes could help me extract the valid cell barcode in Cell Ranger output file singlecell.csv. But the format of singlecell.csv file has been changed after Cell Ranger version 2.0. In version before 2.0, there was column named cell_id and ArchR used command below to recognize valid barcode:

df[which(paste0(df$cell_id) != "None"),]$barcode

While after Cell Ranger version 2.0, the cell_id column has been deprecated. The new column is_cell_barcode was used to show valid barcode. So could you please modify the code to compatible with the new format?

[rcorces]

Hi @cherrie-g! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.