sRNAPipe-cli

sRNAPipe version 1.2.1

Requirements:

• Perl modules:
  • Statistics
  • Parallel::ForkManager
  • Statistics::R
  • Getopt::Long
  • String::Random
  • File::Copy::Recursive
  • Math::CDF
• BWA aligner, version 0.7.12 or higher
• BedTools, version 2.24.0 or higher
• Samtools, version 1.5
• R, version 3.1 or higher
• R packages:
  • plotrix
  • bioconductor-sushi
  • RColorBrewer
  • ggplot2

Install:

Run:

perl Makefile.pl
make install

Usage:

srnapipe --fastq <fastq file 1> --fastq_n <name 1> [--fastq <fastq file 2> --fastq_n <name 2> --fastq <fastq file 3> -- fastq_n <name 3> ...] --ref <reference genome> [--build_index] --transcripts <transcripts> [--build_transcripts] --TE <transposable elements> [--build_TE] --miRNAs <miRNAs> [--build_miRNAs] --snRNAs <snRNAs> [--build_snRNAs] --rRNAs <rRNAs> [--build_rRNAs] --tRNAs <tRNAs> [--buid_tRNAs] --dir <results directory> --html <results.html> [options]

Arguments:

Argument	Description
–fastq	Fastq file to process
–fastq_n	Name of the content to process
–ref	Fasta file containing the reference genome
–transcripts	Fasta file containing the transcripts
–TE	Fasta file containing the transposable elements
–miRNAs	Fasta file containing the miRNAs
–snRNAs	Fasta file containing the snRNAs
–rRNAs	Fasta file containing the rRNAs
–tRNAs	Fasta file containing the tRNAs
–html	Main HTML file where results will be displayed
–dir	Folder where results will be stored

For any fasta file, if a bwa index is not provided, you should build it through the corresponding ‘–build_[element]’ argument

Options:

Option	Description
–min <INT>	Minimum read size (default: 18)
–max <INT>	Maximum read size (default: 29)
–si_min <INT>	Lower bound of siRNA range (default: 21)
–si_max <INT>	Higher bound of siRNA range (default: 21)
–pi_min <INT>	Lower bound of piRNA range (default: 23)
–pi_max <INT>	Higher bound of piRNA range (default: 29)
–mis <INT>	Maximal genome mismatches (default: 0)
–misTE <INT>	Maximal TE mismatches (default: 3)
–PPPon <true|false>	Ping-pong partners (default: true)