annotate README.rst @ 1:20d9fb1ba210 default tip

Replace several tabular manipulations with regex_replace tool

This package contains a Galaxy workflow that reduces a reference protein sequence database by retaining only the sequences that are detected at significant levels in the RNA-seq sample.
The workflow uses RSEM to quantify transcripts in an RNA-seq sample.

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_reduced_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


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

* ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.chromosome.[1-9XY]*.fa.gz
* ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz
* ftp://ftp.ensembl.org/pub/release-73/gtf/mus_musculus/Mus_musculus.GRCm38.73.gtf.gz



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

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

* http://toolshed.g2.bx.psu.edu/view//jjohnson/rsem
* http://toolshed.g2.bx.psu.edu/view/devteam/fasta_formatter


History
=======

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Version Changes
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v0.0.1  - Initial release to Tool Shed (March, 2014)
v0.0.2  - Use regex_replace tool for tabular file manipulation
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