Single-cel ATAC preliminary analysis reports

[rroutsong]

Preliminary pipeline for scATAC analysis using:

R 4.5.0
Seurat 5.4.0
SeuratObject 5.3.0
Signac 1.16.0
GenomeInfoDb 1.46.2
GenomicAlignments 1.46.0
GenomicRanges 1.62.1
rtracklayer 1.70.1

I am awaiting pipeline results, once that has finished and no errors occur along with all reviewers approving I will merge this pull request.

[tovahmarkowitz]

Hi Ryan,

This looks really great. Just a few details:

1. The blacklist ratio calculation lines are slightly different between the two .R scripts. I'm guessing it's because there isn't a blacklist file for mm39, which might have caused you some issues and I had totally forgotten about. Can you make them match? I'm guessing we want the version found in the single-sample file to also be in the multi-sample file. Also, what happens right now if the reference genome is mm39?

2. The "help" sections for the two files should match and not mention spaceranger or RNA.

Otherwise, everything else makes total sense to me. Thanks for all your hard work!

Tovah

[rroutsong]

Hi Ryan,

This looks really great. Just a few details:

1. The blacklist ratio calculation lines are slightly different between the two .R scripts. I'm guessing it's because there isn't a blacklist file for mm39, which might have caused you some issues and I had totally forgotten about. Can you make them match? I'm guessing we want the version found in the single-sample file to also be in the multi-sample file. Also, what happens right now if the reference genome is mm39?
2. The "help" sections for the two files should match and not mention spaceranger or RNA.

Otherwise, everything else makes total sense to me. Thanks for all your hard work!

Tovah

Feel free to change anything after I have finished building the pipeline