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author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents 423ad61697c4 de357bab306d
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1 README 1 riboseqr_wrapper
2 ------ 2 ================
3
4 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_ 3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
5 integration for `Galaxy <http://galaxyproject.org/>`_ / 4 integration for `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_ and `Galaxy <http://galaxyproject.org/>`_.
6 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
7 5
8 Included tools 6 Included tools
9 .............. 7 --------------
10 In the order in which they are run 8 In the order they are run
11 9
12 #. Prepare riboSeqR Input 10 #. Plot triplet periodicity for different read lengths.
13
14 Prepare riboSeqR format input files from alignment files (SAM format,
15 Ribo-Seq or RNA-Seq alignments).
16
17 #. Triplet Periodicity
18
19 Plot triplet periodicity for different read lengths.
20 11
21 #. Metagene Analysis 12 #. Metagene Analysis
22 13
23 Metagene analysis. 14 Metagene analysis.
24 15
31 Differential Translation Analysis 22 Differential Translation Analysis
32 23
33 Get Ribo and RNA-Seq counts with riboSeqR. Perform differential 24 Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
34 translation analysis with baySeq. 25 translation analysis with baySeq.
35 26
36 Tested with 27 Dependencies
37 ........... 28 ------------
38 **R** ``3.1.2`` 29 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit.
39 30
40 **riboSeqR** ``1.0.5`` 31 R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``.
41 32
42 **baySeq** ``2.0.50`` 33 How to test
34 -----------
35 1. Upload the following test data files from the test-data folder.
43 36
44 **rpy2** ``2.3.10`` 37 Prepare riboSeqR input (R data file)
38
39 rsem_chlamy236_deNovo.transcripts.fa
40
41 2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input"
42 can currently be tested using this workflow. Import this workflow into Galaxy.
43
44 3. Run workflow
45
46 In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input.
47
48 In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input.
49
50 Run workflow.
51
52
53 About the test data files
54 .........................
55 The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the
56 riboSeqR package. The commands used were ::
57
58 library(riboSeqR)
59
60 datadir <- system.file("extdata", package = "riboSeqR")
61 chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
62
63 fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
64
65 ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
66 rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
67
68 riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))
69 save(riboDat, file="Prepare riboSeqR input (R data file)")
70
71 rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package.
72
73 Bugs/Issues?
74 ------------
75 Please report here https://github.com/vimalkumarvelayudhan/riboseqr_wrapper/issues