# HG changeset patch # User Vimalkumar Velayudhan # Date 1437489622 -3600 # Node ID b2eb07000039de5edfc5d2f33025240e45624ab8 # Parent 4419c2f77b60816baf232951bcb557e75e644852 Fix spacing in environment_variables in tool_dependencies (breaks env.sh) Cleanup help sections. diff -r 4419c2f77b60 -r b2eb07000039 metagene.xml --- a/metagene.xml Tue Jul 21 14:58:34 2015 +0100 +++ b/metagene.xml Tue Jul 21 15:40:22 2015 +0100 @@ -148,18 +148,18 @@ #. Select *Triplet periodicity (R data file)* from the previous step. #. Specify length of ribosome footprint reads to be used in filtering -(lengths). Only these reads **will** be used in the analysis. + (lengths). Only these reads **will** be used in the analysis. #. Specify frames to consider. This information can be obtained -from the *Triplet periodicity (HTML report)*. + from the *Triplet periodicity (HTML report)*. -.. class:: warningmark + .. class:: warningmark -Please note that the frames specified should correspond to the -lengths of the reads. + Please note that the frames specified should correspond to the + lengths of the reads. #. Under *plotCDS parameters*, input length of footprints to be considered for -generating the plot. + generating the plot. #. Review/change other options if necessary and execute program. @@ -169,12 +169,12 @@ #. Metagene analysis (HTML report) -A HTML file with results and links to other output files - plots for -specified lengths (PDF) and R script used for the session. + A HTML file with results and links to other output files - plots for + specified lengths (PDF) and R script used for the session. #. Metagene analysis (R data file) -Used as input for the next step - *Plot Rribosome Profile*. + Used as input for the next step - *Plot Rribosome Profile*. riboSeqR functions used ....................... diff -r 4419c2f77b60 -r b2eb07000039 prepare.xml --- a/prepare.xml Tue Jul 21 14:58:34 2015 +0100 +++ b/prepare.xml Tue Jul 21 15:40:22 2015 +0100 @@ -105,12 +105,12 @@ This tool can be used to prepare input data for riboSeqR from SAM format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can -do this alignment manually using bowtie or the +do this alignment manually using bowtie or using the "Transcriptome Mapping" -> "Align to transcriptome using Bowtie" tool on `RiboGalaxy <http://ribogalaxy.ucc.ie>`_. The required input format for riboSeqR is mentioned in the -*"Getting Data"* section of the documentation. +"Getting Data" section of the documentation. How to use? ----------- @@ -126,28 +126,34 @@ The following files will be generated on completion: #. Prepare riboSeqR input (HTML report) - A HTML file with links to all other -output files. + output files. + +#. Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided). + These files are plain text and lines have the following information - + strand, transcript name, alignment position, sequence. -* Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided). -These files are plain text and lines have the following information - -strand, transcript name, alignment position, sequence. + .. class:: infomark -Please note the alignments are made *0-indexed*. + Please note the alignments are made **0-indexed**. Additional information on + how the SAM alignments are processed can be found below. -* R script used in this session. +#. R script used in this session. #. Prepare riboSeqR input (R data file) - used as input for the next step - -*Triplet Periodicity*. + *Triplet Periodicity*. How are the SAM alignments processed? ..................................... #. Lines starting with ``@`` are ignored. + #. Lines having a ``FLAG=0`` are considered as successful alignments. These are -considered for the next step. + considered for the next step. + #. Alignment start is located on ``column 4``. These are decremented by -1 as SAM alignments are 1-indexed. + 1 as SAM alignments are 1-indexed. + #. riboSeqR input file is written with the strand (``+``), transcript name, -alignment start and the aligned sequence. + alignment start and the aligned sequence. riboSeqR functions used ....................... diff -r 4419c2f77b60 -r b2eb07000039 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 21 14:58:34 2015 +0100 +++ b/tool_dependencies.xml Tue Jul 21 15:40:22 2015 +0100 @@ -33,18 +33,10 @@ python setup.py build --r-home $R_HOME --r-home-lib $R_HOME/lib install --install-lib $INSTALL_DIR/lib/python - - $INSTALL_DIR/lib/python - - - $ENV[READLINE_LIB_PATH] - - - $ENV[RHOME]/lib - - - $ENV[R_ROOT_DIR]/lib - + $INSTALL_DIR/lib/python + $ENV[READLINE_LIB_PATH] + $ENV[RHOME]/lib + $ENV[R_ROOT_DIR]/lib diff -r 4419c2f77b60 -r b2eb07000039 triplet.xml --- a/triplet.xml Tue Jul 21 14:58:34 2015 +0100 +++ b/triplet.xml Tue Jul 21 15:40:22 2015 +0100 @@ -108,10 +108,10 @@ #. Prepare riboSeqR input (R data file) from the previous step. #. FASTA format file of the reference transcriptome. -.. class:: infomark + .. class:: infomark -Please note that the FASTA header of the transcriptome sequences must -match the sequence names from the SAM file. + Please note that the FASTA header of the transcriptome sequences must + match the sequence names from the SAM file. How to use? ----------- @@ -128,12 +128,12 @@ #. Triplet periodicity (HTML report) -A HTML file with results and links to other output files - triplet -periodicity plot (PDF) and R script used for the session. + A HTML file with results and links to other output files - triplet + periodicity plot (PDF) and R script used for the session. #. Triplet periodicity (R data file) -Used as input for the next step - *Metagene analysis*. + Used as input for the next step - *Metagene analysis*. riboSeqR functions used .......................