Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

annotate README.rst @ 6:5a242f289347 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Merge
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents 423ad61697c4 de357bab306d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
1 riboseqr_wrapper
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
2 ================
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
4
de357bab306d Update README
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 3
diff changeset
4 integration for `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_ and `Galaxy <http://galaxyproject.org/>`_.
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
5
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
6 Included tools
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
7 --------------
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
8 In the order they are run
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
9
6
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 5 4
diff changeset
10 #. Plot triplet periodicity for different read lengths.
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
11
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
12 #. Metagene Analysis
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
13
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
14 Metagene analysis.
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
15
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
16 #. Plot Ribosome Profile
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
17
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
18 Plot Ribosome profile and output Ribo/RNA counts.
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
19
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
20 [OR]
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
21
5
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
22 Differential Translation Analysis
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
23
423ad61697c4 Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero).
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
24 Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
25 translation analysis with baySeq.
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
26
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
27 Dependencies
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
28 ------------
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
29 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
30
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
31 R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
32
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
33 How to test
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
34 -----------
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
35 1. Upload the following test data files from the test-data folder.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
36
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
37 Prepare riboSeqR input (R data file)
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
38
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
39 rsem_chlamy236_deNovo.transcripts.fa
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
40
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
41 2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input"
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
42 can currently be tested using this workflow. Import this workflow into Galaxy.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
43
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
44 3. Run workflow
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
45
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
46 In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
47
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
48 In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input.
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
49
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
50 Run workflow.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
51
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
52
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
53 About the test data files
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
54 .........................
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
55 The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
56 riboSeqR package. The commands used were ::
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
57
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
58 library(riboSeqR)
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
59
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
60 datadir <- system.file("extdata", package = "riboSeqR")
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
61 chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
62
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
63 fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
0
c34c364ce75d First commit
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
diff changeset
64
3
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
65 ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
66 rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
67
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
68 riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
69 save(riboDat, file="Prepare riboSeqR input (R data file)")
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
70
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
71 rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package.
d7ce95ccf54f Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 0
diff changeset
72
4
de357bab306d Update README
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 3
diff changeset
73 Bugs/Issues?
de357bab306d Update README
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 3
diff changeset
74 ------------
de357bab306d Update README
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 3
diff changeset
75 Please report here https://github.com/vimalkumarvelayudhan/riboseqr_wrapper/issues