scsit-tools 1.0.1

Biological gene analyse tool

Introduction

SCSit: A high-efficiency cell types identification tool for single-cell sequencing data from SPLiT-seq

Parameter description

All file_path are Absolute path, cause thread work direction may different with file path. So path from content root is not suitable here.

Eg:

  Program: SCSit (A high-efficiency preprocessing tool for single-cell sequencing data from SPLiT-seq)
  
  Contact: Shangqian Xie <[e-mail]>
    Usage: SCSit [options] -r1 input_r1.fastq -r2 input_r2.fastq -p primer.list -b barcode.list -o output
    
  params:
    "       -r1 R1File        Paths to files that contain input read1 of SPLiT-seq pair-end files
    "       -r2 R2File        Paths to files that contain input read2 of SPLiT-seq pair-end files
    "       -p primerList     Primer list of all oligonucleotide sequences used
    "       -b barcodeList    The 96 well plate oligonucleotides used for each round of barcodes
    Options:
    "       -t int            Maximum number of threads to use [default:4]
    "       -o output_prefix  Paths to files that contain output file prefix [default:output]
    "       -h                show this help message and exit