moving from merging scATAC pipeline to Analyzing PBMC scATAC-seq pipeline

[pengxin2019]

Hi Tim,
I have finished merging two scATAC datasets using this pipeline (https://satijalab.org/signac/articles/merging.html). Now, I am moving to the Analyzing PBMC scATAC-seq (https://satijalab.org/signac/articles/merging.html). (By the way, feel free to correct me if you think this combination of pipeline is not proper).

However, I am stuck in the step below (second pipeline mentioned above) since there is no peak_region_fragments column or blacklist_region_fragments column or peak_region_fragments in the "pbmc" object.

add blacklist ratio and fraction of reads in peaks

pbmc$pct_reads_in_peaks <- pbmc$peak_region_fragments / pbmc$passed_filters * 100
pbmc$blacklist_ratio <- pbmc$blacklist_region_fragments / pbmc$peak_region_fragments

In the merging pipeline, the "pbmc500.counts" object does not have those three columns which is included in the "md.500". So, I think this is a little gap between these two pipeline. Can you give me some suggestions on how to transfer these three columns to the pbmc which is a Seurat Object? I am new to it

Thanks

[timoast]

Those metadata values are present in the per-cell metadata computed by 10x cellranger-atac. To include that information, set the meta.data field in CreateSeuratObject() as shown in the vignettes, or use the AddMetaData() function.