Mercurial > repos > galaxyp > proteomics_rnaseq_reduced_db_workflow
changeset 0:9d5e59373c84
Initial upload
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 17 Mar 2014 16:03:12 -0500 |
| parents | |
| children | 20d9fb1ba210 |
| files | README.rst proteomics_rnaseq_reduced_db_workflow.ga repository_dependencies.xml |
| diffstat | 3 files changed, 746 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Mar 17 16:03:12 2014 -0500 @@ -0,0 +1,52 @@ +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) +======= ====================================================================== + +
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