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Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero). readingFrame function fails with subscript out of bounds. Bugfix 2: [triplet] Check if transcript name in SAM matches the name in FASTA. Produce an error message if it's not. This fixes the problem where an empty plot is produced (no bars). [ribosome_profile] - A proper error message is now produced if an invalid transcript name is provided. Updated test data
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:21:50 +0000
parents c34c364ce75d
children 5a242f289347
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1 riboseqr_wrapper 1 README
2 ---------------- 2 ------
3
3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_ 4 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
4 integration for `Galaxy <http://galaxyproject.org/>`_ and 5 integration for `Galaxy <http://galaxyproject.org/>`_ /
5 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_. 6 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
6 7
7 Included tools 8 Included tools
8 .............. 9 ..............
9 In the order they are run 10 In the order in which they are run
10 11
11 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files. 12 #. Prepare riboSeqR Input
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).
14 13
15 2. Triplet Periodicity - Plot triplet periodicity for different read lengths. 14 Prepare riboSeqR format input files from alignment files (SAM format,
15 Ribo-Seq or RNA-Seq alignments).
16 16
17 3. Metagene Analysis 17 #. Triplet Periodicity
18 18
19 4. Plot Ribosome Profile 19 Plot triplet periodicity for different read lengths.
20
21 #. Metagene Analysis
22
23 Metagene analysis.
24
25 #. Plot Ribosome Profile
26
27 Plot Ribosome profile and output Ribo/RNA counts.
20 28
21 [OR] 29 [OR]
22 30
23 Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential 31 Differential Translation Analysis
32
33 Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
24 translation analysis with baySeq. 34 translation analysis with baySeq.
25 35
26 Dependencies 36 Tested with
27 ............ 37 ...........
28 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64.
29
30 **R** ``3.1.2`` 38 **R** ``3.1.2``
31 39
32 **riboSeqR** ``1.0.5`` 40 **riboSeqR** ``1.0.5``
33 41
34 **baySeq** ``2.0.50`` 42 **baySeq** ``2.0.50``