STARsolo --EmptyDrops_CR parameters
I'm having some issues with the alignment of 10x scRNAseq data to a custom genome and I thought it would be good to do a stricter filtering on the cells so more cells get filtered out as empty droplets. Apparently STARsolo has several filtering algorithms, of which the EmptyDrops one is most similar to the CellRanger filtering. The manual lists 10 different parameters, but I can't make sense of what they mean and there's no further explanation.
In STARsolo, this filtering can be activated by:
--soloCellFilter EmptyDrops_CR. It can be followed by 10 numeric parameters: nExpectedCells (3000), maxPercentile (0.99), maxMinRatio (10), indMin (45000), indMax (90000), umiMin (500), umiMinFracMedian (0.01), candMaxN (20000), FDR (0.01), simN (10000).
Now if I just want a stricter threshold on e.g. UMIs/cell for the filtering (see picture), should I increase umiMin or also set anything else? If someone can provide a full explanation of the parameters that would also be great.
EDIT: I'm also having an error when running
STAR --runMode soloCellFiltering $RAW_COUNT_PATH $OUT_PATH --soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 10000 0.01 20000 0.01 10000.
STAR_filter_solo_PI3K.sh: line 35: 3321 Segmentation fault (core dumped) STAR --runMode soloCellFiltering $RAW_COUNT_PATH $OUT_PATH --soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 10000 0.01 20000 0.01 10000
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