search

bartosovic-lab / nanoscope

MIT License
1 stars 2 forks source link

fragments_noLA_duplicates #5

Open Guliariel opened 5 months ago

Guliariel commented 5 months ago

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

bartosovic-lab commented 4 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.