QC matrix

[HaniJieunKim]

Hi, thanks for creating a very useful pacakge!

I'd like to run scone on a scRNA-seq dataset. But I do not have many of the information found in the quality matrix in the tutorial example data (fluidigm).

colnames(qc)
 [1] "NREADS"                      
 [2] "NALIGNED"                    
 [3] "RALIGN"                      
 [4] "TOTAL_DUP"                   
 [5] "PRIMER"                      
 [6] "INSERT_SZ"                   
 [7] "INSERT_SZ_STD"               
 [8] "COMPLEXITY"                  
 [9] "NDUPR"                       
[10] "PCT_RIBOSOMAL_BASES"         
[11] "PCT_CODING_BASES"            
[12] "PCT_UTR_BASES"               
[13] "PCT_INTRONIC_BASES"          
[14] "PCT_INTERGENIC_BASES"        
[15] "PCT_MRNA_BASES"              
[16] "MEDIAN_CV_COVERAGE"          
[17] "MEDIAN_5PRIME_BIAS"          
[18] "MEDIAN_3PRIME_BIAS"          
[19] "MEDIAN_5PRIME_TO_3PRIME_BIAS"

Is there a way to generate this from the scRNA-seq dataset (count data)? I do not have access to the raw pre-aligned data.

Thanks!

Best regards,

Hani