timoast
commented
4 years ago If I understand correctly, you're saying that you find fewer differentially accessible peaks when using cellranger aggr to combine datasets, compared with merging the data? Cellranger aggr downsamples the reads to an equal level across the batches, so it's expected that you would lose some sensitivity. Note that we don't recommend performing differential expression or accessibility using integrated data, for explanation see several closed issues in the Seurat package
Hi Tim, I found lots of differential peak, the number about two or three thousand, which Base on the Standard workflow of integrated data in Signac. nevertheless, The less differential peak, just twenty or thirty ,found using cell-atac aggr for integrated data. why the number of differential peak is significantly different about on two integrated way? Thanks