Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper
diff prepare.xml @ 2:b2eb07000039
Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Cleanup help sections.
| author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
|---|---|
| date | Tue, 21 Jul 2015 15:40:22 +0100 |
| parents | c34c364ce75d |
| children |
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--- 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 .......................