Open Guliariel opened 5 months ago
Hi,
By default the cell picking script is using all reads including PCR duplicates, which from my experience is the preferred way of calling cells, so I think it's no issue there. In case of such large number of LA duplicates, it's probably better to construct the region x cell matrix using the $SAMPLE_ID/$MODALITY_$BARCODE/cellranger/outs/fragments_noLA_duplicates.tsv.gz
fragments file, but you can also try to use both duplicated and non-duplicated fragments file and see if it makes any difference. In case of low number of LA duplicates it did not for us. Hope this helps.
Hello and thank you for this excellent documentation.
I've have encountered over 25% lateral amplification duplicates. I'm curious whether the "downstream analysis" takes into account the cell_pick script or solely during the creation of the Seurat object (after all the cells were re-called)?
Appreciatively, Gal