Update README.md

README.md

@@ -140,9 +140,15 @@ python marine.py \
 --output_folder examples/sc_subset_CT \
 --barcode_whitelist_file examples/data/sc_barcodes.tsv.gz \
 --barcode_tag "CB" \
---strandedness 2
+--strandedness 2 \
+--all_cells_coverage # This flag will generate barcode x position coverage matrices.
 ```
 
+A recommended workflow for single-cell:
+* Run MARINE without the --all_cells_coverage flag set
+* Filter resulting edit sites down to a set you want to proceed with
+* Only run --all_cells_coverage in tandem with --tabulation_bed, which is where you can specify which sites should have coverage calculated across all cells. Otherwise this bit could take a very long time.
+
 # Single cell long read example
 
 MARINE can be used to calculate edits and coverage on a per-cell and per-isoform basis after certain pre-processing steps are taken. Reads can be quantified and assigned to annotated isoforms using IsoQuant (v3.3.0) with parameters: --data-type pacbio, --transcript_quantification unique_only, and --gene_quantification unique_only. The read assignment output from IsoQuant can be used to add an isoform tag for each read, indicating the isoform to which it was assigned. Furthermore, the cell barcode can be concatenated to the isoform in a new tag called "IB", as shown in the IGV screenshot below (grouping labels refer to this tag in this case). Note that a suffix has been added to each IB tag reflecting the ending of both the isoform ID and the cell barcodes, which is used for efficiently calculating coverage only within each appropriate subset of isoform and cell-specific reads.