Data processing for Smart-seq2 data

[arshiyaakeel]

Hello,

I am new in the area of single cell RNA seq data analysis.I have 50 fastq files for a single sample from the Smart-seq2 platform.
I would like to generate a count matrix of expression for these files.
I did not find any example to process smart-seq2 data from the tutorial

http://bioinf.wehi.edu.au/scPipe/

Is it posible to use scPipe for Smart-seq2?

Thank you very much.

Best regards
Arshiya