Alternative entrypoint?

[colindaven]

Hi,

I don't use Cellranger since we have BD Rhapsody data which is not compatible.

Is there a way to input the data into this tool after generating the count matrix, but before standard normalization, reporting etc ?
In other words, I don't want to start with fastqs, but with a matrix.

Thanks

[zhangjing1123]

If you need to input a csv format expression matrix file, this can be achieved by modifying the corresponding parameters in the following configuration file:
[indata]
s1="path/s1_matrix.csv"
s2="path/s2_matrix.csv"
[run]
fastp=false
cellrangle=false
[step1]
filetype="csv"
csv_sep=","

Set the path of the expression matrix corresponding to each sample in [indata]
Set fastp and cellranger to false in [run] to skip these two steps
Set the input file type to csv and the separator to comma in [step1]