I'm a newbie in single cell and I a need to pre process some samples. Recently I did it with cellRanger count and it went fine with good results, but now my data was builded with a chemistry I have never seen before, I have 8 bp for I 25 bp for R1 and 90 bp for R2. The colleague who sent me the data says it was made with chemistry v2 but after after a few attempts it has been impossible to get the counts with cellranger count. I have read that cellranger needs at least 26 bp (barcode+UMI) in R1 to works properly.
Does anyone know how I should preprocess this data? and if it is possible to do it with cellranger?