Hashed Drops
Hashed Drops is a demultiplexing tool part of the library Droplet Utils. More information can be found at:
Hashed Drops by Droplet Utils: Hashed Drops .
| Parameter | Description | Example |
|---|---|---|
| hashtag_data | path to filtered HTO matrix | –hashtag_data “path/hto_filtered/” |
| rawData | TRUE if the HTO matrix is raw data to execute hashed drops first | –rawData FALSE |
| ambient | Only available when the dataset specifies the relative abundance of each HTO in the ambient solution (results from empty drops), otherwise keep in NULL | –ambient “NULL” |
| minProp | Numeric scalar to be used to infer the ambient profile when ambient=NULL | –minProp 0.05 |
| pseudoCount | minimum pseudo-count when computing log-fold changes. | –pseudoCount 5 |
| constAmbient | Indicates whether a constant level of ambient contamination should be used to estimate LogFC2 for all cell | –constAmbient FALSE |
| doubletMin | Specifies the minimum threshold on the log-fold change to use to identify doublets | –doubletMin 2 |
| doubletNmads | specifies the number of median absolute deviations (MADs) to use to identify doublets. | –doubletNmads 3 |
| confidenMin | specifying the minimum threshold on the log-fold change to use to identify singlet | –confidenMin 2 |
| confidentNmads | specifies the number of MADs to use to identify confidently assigned singlets | –confidentNmads 3 |
The description of this parameters were provided by the library. They can also be found in the link above.