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This is package is a Galaxy workflow for the detection and incorporation of novel splice sequences into custom splice-junction databases. 

The splice database workflow first aligns RNA-Seq data to the genome twice, first to only those splice junctions found in the Ensembl gene models and second to both the Ensembl gene models and reference genome.  The output BED files, which contain the coordinates of all detected junctions, are compared and only those coordinates for splice junctions not present in the gene models are retrieved.  Next, the genomic sequences for each splice junction is retrieved.  We developed a program, "Translate BED sequences", which translates the splice junctions and compiles all splice-junction polypeptide sequences of the user's choice.  The user may choose to filter out splice junction entries that contain stop codons, are less than a certain length, and are below a certain expression level measured by splice-junction RNA-Seq read depth.

See http://www.galaxyproject.org for information about the Galaxy Project.


Availability
============

This workflow is available to download and/or install from the main
Galaxy Tool Shed:

http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_splice_db_workflow


Reference Data
==============

For Human RNAseq data this workflow was tested using reference data from:

* ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.chromosome.[1-9XY]*.fa.gz
* ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz
* ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz


Dependencies
============

These dependencies should be resolved automatically via the Galaxy Tool Shed:

* http://toolshed.g2.bx.psu.edu/view/devteam/tophat
* http://toolshed.g2.bx.psu.edu/view/jjohnson/filter_bed_on_splice_junctions
* http://toolshed.g2.bx.psu.edu/view/jjohnson/translate_bed_sequences


History
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Version Changes
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v0.0.1  - Initial release to Tool Shed (March, 2014)
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