diff README.rst @ 0:9d5e59373c84

Initial upload

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