Using VarTrix on long-read single cell sequencing data

[haghani-sara]

Hi, I'm just wondering if VarTrix can be used for variant detection in ONT long-read data or is it just exclusively for short-read single cell sequencing data? Has anyone tried this and succeeded?

[modalaigh]

Hi, I've used VarTrix successfully with PacBio long-read Kinnex scRNA-seq data

[haghani-sara]

Hi, I've used VarTrix successfully with PacBio long-read Kinnex scRNA-seq data

@modalaigh do you mind sharing more about how you did that? I'm specifically interested in the pipeline you used (if any) to get the cell barcodes file. When I tried using Vartrix for my ONT long read 10x scRNA-seq, the cell barcode file didn't seem to be compatible. I suspect because it's not the output of cellranger pipeline.

[modalaigh]

Hi, the PacBio SMRT Link pipeline that was used to process the Kinnex scRNA-seq data produced a list of barcodes that I used as input for VarTrix. I'm not too familiar with ONT's scRNA-seq methods - did you use their method which uses 10x-generated cDNA as input?