This repository contains scripts to organize sequencing data.
Use the conda environment environment_1.
- organize fastq files into subfolders of the main sequencing project, and having the pair mates R1 and R2 together (in paired-end sequencing)
- store fastqc files in proper directory
- calling cell ranger count to generate the count matrix
- get the reverse complement sequence of index i5 for SMART-seq demultiplexing file