|
0
|
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.
|
|
|
7
|
|
|
8
|
|
|
9 Availability
|
|
|
10 ============
|
|
|
11
|
|
|
12 This workflow is available to download and/or install from the main
|
|
|
13 Galaxy Tool Shed:
|
|
|
14
|
|
|
15 http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_sap_db_workflow
|
|
|
16
|
|
|
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:
|
|
|
22
|
|
|
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
|
|
|
26
|
|
|
27
|
|
|
28 For Mouse RNAseq data this workflow was tested with a genome build named "GRCm38_canon" using reference data from:
|
|
|
29
|
|
|
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
|
|
|
33
|
|
|
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.
|
|
|
38
|
|
|
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 ======= ======================================================================
|
|
|
59
|
|
|
60
|
