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README.rst proteomics_rnaseq_human_splice_db_workflow.ga proteomics_rnaseq_mouse_splice_db_workflow.ga proteomics_rnaseq_splice_db_workflow.ga repository_dependencies.xml |
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| diff -r 000000000000 -r 3a11830963e3 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Mar 17 15:59:57 2014 -0500 |
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| @@ -0,0 +1,60 @@ +This package contains a Galaxy workflow for the detection and incorporation of single amino acid polymorphism (SAP) into a custom proteomics search database. + +The workflow aligns RNA-Seq reads to the organism's genome using Tophat, call SNPs using SAMtools mpileup command, and annotates the SNPs that reside within protein-coding regions using SNPeff. +Galaxy tool "SNPeff to Peptide Fasta" generates peptide sequences with the polymorhisms. + +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_sap_db_workflow + + +Reference Data +============== + +For Human RNAseq data this workflow was tested with a genome build named "GRCh37_canon" 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 with a genome build named "GRCm38_canon" 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 + + +Genome builds "GRCh37_canon" and "GRCm38_canon" were built according to instructions in: https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +The builds used only the standard chromosomesi sequences from the reference fasta; the other sequences were filtered out. +The GTF was filtered to retain only those entries that referenced the standard chromosomes. + + +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/devteam/samtools_mpileup +* http://toolshed.g2.bx.psu.edu/view/nilesh/bcftools +* http://toolshed.g2.bx.psu.edu/view/iuc/snpeff +* http://toolshed.g2.bx.psu.edu/view/jjohnson/snpeff_to_peptides + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial release to Tool Shed (March, 2014) +======= ====================================================================== + + |
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| diff -r 000000000000 -r 3a11830963e3 proteomics_rnaseq_human_splice_db_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomics_rnaseq_human_splice_db_workflow.ga Mon Mar 17 15:59:57 2014 -0500 |
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| diff -r 000000000000 -r 3a11830963e3 proteomics_rnaseq_mouse_splice_db_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomics_rnaseq_mouse_splice_db_workflow.ga Mon Mar 17 15:59:57 2014 -0500 |
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| diff -r 000000000000 -r 3a11830963e3 proteomics_rnaseq_splice_db_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomics_rnaseq_splice_db_workflow.ga Mon Mar 17 15:59:57 2014 -0500 |
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| b |
| diff -r 000000000000 -r 3a11830963e3 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Mar 17 15:59:57 2014 -0500 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<repositories description="Required tools for proteomics_rnaseq_splice_db_workflow"> + <repository name="tophat" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="1030acbecce6" /> + <repository name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="44a18a94d7a9" /> + <repository name="bcftools" owner="nilesh" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3182c7fac413" /> + <repository name="snpeff" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="e8adfc4c0a6b" /> + <repository name="snpeff_to_peptides" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="fcb7188fa0d2" /> +</repositories> |