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]