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)