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?
ArchR has built-in support for Harmony correction;
projHeme2 <- addHarmony(
ArchRProj = projHeme2,
reducedDims = "IterativeLSI",
name = "Harmony",
groupBy = "dataset"
)
https://www.archrproject.com/bookdown/batch-effect-correction-wtih-harmony.html
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.
Thank you so much LChart!
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