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1 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.
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2 The workflow uses RSEM to quantify transcripts in an RNA-seq sample.
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3
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4 See http://www.galaxyproject.org for information about the Galaxy Project.
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5
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6
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7 Availability
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8 ============
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9
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10 This workflow is available to download and/or install from the main
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11 Galaxy Tool Shed:
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12
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13 http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_reduced_db_workflow
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14
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15
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16 Reference Data
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17 ==============
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18
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19 For Human RNAseq data this workflow was tested using reference data from:
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20
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21 * ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.chromosome.[1-9XY]*.fa.gz
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22 * ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz
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23 * ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz
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24
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25
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26 For Mouse RNAseq data this workflow was tested using reference data from:
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27
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28 * ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.chromosome.[1-9XY]*.fa.gz
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29 * ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz
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30 * ftp://ftp.ensembl.org/pub/release-73/gtf/mus_musculus/Mus_musculus.GRCm38.73.gtf.gz
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31
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32
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33
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34 Dependencies
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35 ============
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36
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37 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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38
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39 * http://toolshed.g2.bx.psu.edu/view//jjohnson/rsem
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40 * http://toolshed.g2.bx.psu.edu/view/devteam/fasta_formatter
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41
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42
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43 History
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44 =======
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45
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46 ======= ======================================================================
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47 Version Changes
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48 ------- ----------------------------------------------------------------------
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49 v0.0.1 - Initial release to Tool Shed (March, 2014)
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50 ======= ======================================================================
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51
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52
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