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Initial upload
author Jim Johnson <jj@umn.edu>
date Mon, 17 Mar 2014 15:59:57 -0500
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1 This package contains a Galaxy workflow for the detection and incorporation of single amino acid polymorphism (SAP) into a custom proteomics search database.
2
3 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.
4 Galaxy tool "SNPeff to Peptide Fasta" generates peptide sequences with the polymorhisms.
5
6 See http://www.galaxyproject.org for information about the Galaxy Project.
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8
9 Availability
10 ============
11
12 This workflow is available to download and/or install from the main
13 Galaxy Tool Shed:
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15 http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_sap_db_workflow
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17
18 Reference Data
19 ==============
20
21 For Human RNAseq data this workflow was tested with a genome build named "GRCh37_canon" using reference data from:
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23 * ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.chromosome.[1-9XY]*.fa.gz
24 * ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz
25 * ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz
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27
28 For Mouse RNAseq data this workflow was tested with a genome build named "GRCm38_canon" using reference data from:
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30 * ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.chromosome.[1-9XY]*.fa.gz
31 * ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz
32 * ftp://ftp.ensembl.org/pub/release-73/gtf/mus_musculus/Mus_musculus.GRCm38.73.gtf.gz
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34
35 Genome builds "GRCh37_canon" and "GRCm38_canon" were built according to instructions in: https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
36 The builds used only the standard chromosomesi sequences from the reference fasta; the other sequences were filtered out.
37 The GTF was filtered to retain only those entries that referenced the standard chromosomes.
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39
40 Dependencies
41 ============
42
43 These dependencies should be resolved automatically via the Galaxy Tool Shed:
44
45 * http://toolshed.g2.bx.psu.edu/view/devteam/tophat
46 * http://toolshed.g2.bx.psu.edu/view/devteam/samtools_mpileup
47 * http://toolshed.g2.bx.psu.edu/view/nilesh/bcftools
48 * http://toolshed.g2.bx.psu.edu/view/iuc/snpeff
49 * http://toolshed.g2.bx.psu.edu/view/jjohnson/snpeff_to_peptides
50
51 History
52 =======
53
54 ======= ======================================================================
55 Version Changes
56 ------- ----------------------------------------------------------------------
57 v0.0.1 - Initial release to Tool Shed (March, 2014)
58 ======= ======================================================================
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60