Entering edit mode
7 months ago
bioinformatics.girl ▴ 10
So I'm trying to integrate two datasets together for 10 different samples (taken in different batches). To mitigate for that I looked into Harmony but was not sure how to essentially apply Harmony from two datasets and get fragment files for later analysis in ArchR.
Any suggestions or pointers?
No. I am asking how to merge 2 fragment files *before starting an ArchR project.
I would not recommend doing this, as the fragment files contain the raw data, which will have a batch effect; and there are no mechanisms by which to correct fragments. Even if the fragment files are from technical replicates; in cases where you suspect a batch effect, the recommendation is to keep the files separate, use the built-in correction methodology for clustering; and include the replicate information as a covariate in the final statistical models being used.
If you do not suspect there to be a batch effect (i.e., the same libraries were sequenced multiple times), you can merge the .bam files and re-generate the fragment files from the resulting file.
By the way, if you are using joint RNA + ATAC and trying to use the RNA clusters for ATAC analysis, please specify this in your original description.
Thank you so much LChart!