view README.rst @ 5:423ad61697c4

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

README
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`riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
integration for `Galaxy <http://galaxyproject.org/>`_ /
`RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.

Included tools
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In the order in which they are run

#. Prepare riboSeqR Input

   Prepare riboSeqR format input files from alignment files (SAM format,
   Ribo-Seq or RNA-Seq alignments).

#. Triplet Periodicity

   Plot triplet periodicity for different read lengths.

#. Metagene Analysis

   Metagene analysis.

#. Plot Ribosome Profile

   Plot Ribosome profile and output Ribo/RNA counts.

   [OR]

   Differential Translation Analysis

   Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
   translation analysis with baySeq.

Tested with
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**R** ``3.1.2``

**riboSeqR** ``1.0.5``

**baySeq** ``2.0.50``

**rpy2** ``2.3.10``