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Change R data file format in xml wrappers (rda -> RData) Add test data, sample workflow. Updated README with instructions on testing.
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Wed, 22 Jul 2015 12:07:39 +0100
parents c34c364ce75d
children de357bab306d
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2:b2eb07000039 3:d7ce95ccf54f
1 riboseqr_wrapper 1 riboseqr_wrapper
2 ---------------- 2 ================
3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_ 3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
4 integration for `Galaxy <http://galaxyproject.org/>`_ and 4 integration for `Galaxy <http://galaxyproject.org/>`_ and
5 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_. 5 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
6 6
7 Included tools 7 Included tools
8 .............. 8 --------------
9 In the order they are run 9 In the order they are run
10 10
11 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files. 11 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
12 The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome. 12 The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome.
13 (RNA-Seq data is optional but required for Differential translation analysis). 13 (RNA-Seq data is optional but required for Differential translation analysis).
22 22
23 Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential 23 Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
24 translation analysis with baySeq. 24 translation analysis with baySeq.
25 25
26 Dependencies 26 Dependencies
27 ............ 27 ------------
28 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64. 28 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit.
29 29
30 **R** ``3.1.2`` 30 R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``.
31 31
32 **riboSeqR** ``1.0.5`` 32 How to test
33 -----------
34 1. Upload the following test data files from the test-data folder.
33 35
34 **baySeq** ``2.0.50`` 36 Prepare riboSeqR input (R data file)
35 37
36 **rpy2** ``2.3.10`` 38 rsem_chlamy236_deNovo.transcripts.fa
39
40 2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input"
41 can currently be tested using this workflow. Import this workflow into Galaxy.
42
43 3. Run workflow
44
45 In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input.
46
47 In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input.
48
49 Run workflow.
50
51
52 About the test data files
53 .........................
54 The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the
55 riboSeqR package. The commands used were ::
56
57 library(riboSeqR)
58
59 datadir <- system.file("extdata", package = "riboSeqR")
60 chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
61
62 fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
63
64 ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
65 rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
66
67 riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))
68 save(riboDat, file="Prepare riboSeqR input (R data file)")
69
70 rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package.
71