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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62
author brasset_jensen
date Wed, 06 Feb 2019 04:03:15 -0500
parents 740884893563
children fe3a93edb210
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4 sRNAPipe 4 sRNAPipe
5 ======== 5 ========
6 6
7 A GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data 7 A GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data
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9 Description 10 Description
10 ----------- 11 -----------
11 12
12 The field of small RNA is one of the most investigated research areas since they were shown to regulate gene expression and play essential roles in fundamental biological processes. 13 The field of small RNA is one of the most investigated research areas since they were shown to regulate gene expression and play essential roles in fundamental biological processes.
13 sRNAPipe a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: microRNAs, gene transcripts, small nuclear RNAs, ribosomal RNAs, transfer RNAs and transposable elements. It also provides individual mapping and counting for chromosomes, gene transcripts and transposable elements, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5’-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing numbers of overlaps and corresponding z-scores. 14 sRNAPipe a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: microRNAs, gene transcripts, small nuclear RNAs, ribosomal RNAs, transfer RNAs and transposable elements. It also provides individual mapping and counting for chromosomes, gene transcripts and transposable elements, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5’-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing numbers of overlaps and corresponding z-scores.
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14 16
15 Prerequisites 17 Prerequisites
16 ------------- 18 -------------
17 19
18 1. Unix system with A Galaxy server (release 16.01 or later installed) 20 1. Unix system with A Galaxy server (release 16.01 or later installed)
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27 3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random", "File::Copy::Recursive" and "Math::CDF" installed. 29 3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random", "File::Copy::Recursive" and "Math::CDF" installed.
28 30
29 4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2" installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html 31 4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2" installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html
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31 Installation 34 Installation
32 ------------ 35 ------------
33 36
37 sRNAPipe can be installed through the toolshed.
34 The process has to be completed by an administrator of your Galaxy server to install sRNAPipe. 38 The process has to be completed by an administrator of your Galaxy server to install sRNAPipe.
35 39
40 You can also install the tool manually:
36 41
37 1. Download sRNAPipe 42 1. Download sRNAPipe
38 You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe 43 You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe
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40 2. Put the tool into Galaxy's tools directory 45 2. Put the tool into Galaxy's tools directory
50 <tool file="sRNAPipe.xml" /> 55 <tool file="sRNAPipe.xml" />
51 </section> 56 </section>
52 57
53 4. Start or Restart Galaxy to use it. 58 4. Start or Restart Galaxy to use it.
54 59
60 5. Check that the dependencies are correctly installed through Conda in "Manage dependencies".
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55 User Manual 63 User Manual
56 =========== 64 ===========
57 65
58 .. raw:: html 66 .. raw:: html
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60 <object data="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px"> 68 <object data="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px">
61 <embed src="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf"> 69 <embed src="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">
62 This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p> 70 <p>This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p>
63 </embed> 71 </embed>
64 </object> 72 </object>
65 73