diff 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

--- a/README.rst	Tue Jul 21 15:40:22 2015 +0100
+++ b/README.rst	Tue Oct 27 12:21:50 2015 +0000
@@ -1,32 +1,40 @@
-riboseqr_wrapper
-----------------
+README
+------
+
 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
-integration for `Galaxy <http://galaxyproject.org/>`_ and
+integration for `Galaxy <http://galaxyproject.org/>`_ /
 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
 
 Included tools
 ..............
-In the order they are run
+In the order in which they are run
+
+#. Prepare riboSeqR Input
 
-1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
-   The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome.
-   (RNA-Seq data is optional but required for Differential translation analysis).
+   Prepare riboSeqR format input files from alignment files (SAM format,
+   Ribo-Seq or RNA-Seq alignments).
+
+#. Triplet Periodicity
 
-2. Triplet Periodicity - Plot triplet periodicity for different read lengths.
+   Plot triplet periodicity for different read lengths.
+
+#. Metagene Analysis
 
-3. Metagene Analysis
+   Metagene analysis.
 
-4. Plot Ribosome Profile
+#. 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
+   Differential Translation Analysis
+
+   Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
    translation analysis with baySeq.
 
-Dependencies
-............
-Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64.
-
+Tested with
+...........
 **R** ``3.1.2``
 
 **riboSeqR** ``1.0.5``