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Update README
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Wed, 22 Jul 2015 12:20:16 +0100
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1 riboseqr_wrapper
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2 ================
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3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
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4 integration for `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_ and `Galaxy <http://galaxyproject.org/>`_.
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6 Included tools
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7 --------------
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8 In the order they are run
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10 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
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11 The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome.
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12 (RNA-Seq data is optional but required for Differential translation analysis).
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14 2. Triplet Periodicity - Plot triplet periodicity for different read lengths.
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16 3. Metagene Analysis
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18 4. Plot Ribosome Profile
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20 [OR]
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22 Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
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23 translation analysis with baySeq.
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25 Dependencies
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26 ------------
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27 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit.
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29 R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``.
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31 How to test
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32 -----------
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33 1. Upload the following test data files from the test-data folder.
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35 Prepare riboSeqR input (R data file)
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37 rsem_chlamy236_deNovo.transcripts.fa
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39 2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input"
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40 can currently be tested using this workflow. Import this workflow into Galaxy.
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42 3. Run workflow
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44 In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input.
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46 In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input.
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48 Run workflow.
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51 About the test data files
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52 .........................
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53 The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the
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54 riboSeqR package. The commands used were ::
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56 library(riboSeqR)
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58 datadir <- system.file("extdata", package = "riboSeqR")
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59 chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
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61 fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
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63 ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
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64 rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
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66 riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))
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67 save(riboDat, file="Prepare riboSeqR input (R data file)")
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69 rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package.
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70
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71 Bugs/Issues?
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72 ------------
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73 Please report here https://github.com/vimalkumarvelayudhan/riboseqr_wrapper/issues