@@ -184,6 +184,30 @@ zUMIs has powerful downsampling capabilites. Independent of downsampling mode, t
- downsampling to several depths: Several depths can be requested by comma separation. Combinations of fixed depth and depth ranges may be given. Example: -d 10000,10000-20000,30000
## Cell Barcodes
In order to be compatible with well-based and droplet-based scRNA-seq methods, zUMIs is flexible with handling of cell barcodes.
As default behavior, zUMIs tries to guesstimate the relevant barcodes from the data using the cumulative read distribution ("knee plot").
To override automatic detection of barcodes, users can either give a fixed number of barcodes to consider (e.g. "-b 100") or refer to a plain text file containing known expected barcodes (e.g. "-b barcodefile.txt").
The text file should contain just one column with a list of barcodes without headers and without sample names:
```
ATGAAT
ATCAAA
GGAGCC
TAAGAT
AAAACT
GCGCTG
CCAACC
CTTTAA
TCATAT
TACTAT
```
## Getting help
Please report bugs :beetle::bug: to the [zUMIs Github issue page](https://github.com/sdparekh/zUMIs/issues)
