Including metadata while merging

[Sun-storm]

Hi everyone!

I'm currently working with an scATAC dataset that was run on 4 different lanes. To analyze it I learned that I need to merge them, but the merging tutorial doesn't seem to explain how to also include the metadata.

Do I:
- Include it into each of the 4 datasets and then merge them.
- Or should I merge and then add the metadata.

With the metadata i mean the singlecell.csv mentioned in the tutorials.

I have followed the "Analyzing PBMC scATAC-seq" and the "Merging objects" vignettes, but I can't figure out how to implement the way the metadata is added in the "Analyzing PBMC scATAC-seq" into the "Merging objects" vignette.

Does anybody know how I could do it?

Thank you :)

Edit: I figured out this was a problem when I tried to create a gene activity matrix with the data I had after following the merging tutorial. This is what I got.
> gene.activities <- GeneActivity(combined)
Extracting gene coordinates
Error in eval(bysub, x, parent.frame()) : object 'gene_id' not found

And when I tried to see if I had any annotations:
> head(Annotation(combined))
NULL

[Sun-storm]

I figured it out, just had to include these lines
annotattion = GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevelsStyle(annotation) = "UCSC"

and annotate each SeuratObject you create like this
Annotation(your_seurat_object) = annotation

Before merging the seurat objects together, if anyone ever has the same issue.

To better explain myself, you have to create the annotation, which what the first two lines do (I use the EnsDb.Hsapiens.v86 because I work on human data) and then chose UCSC, but you can choose others I believe.

Then, when you create the seurat objects (step just before merging), you annotate those seurat objects with the last line I just wrote and then merge.