Mercurial > repos > galaxyp > proteomics_rnaseq_reduced_db_workflow
annotate README.rst @ 1:20d9fb1ba210 default tip
Replace several tabular manipulations with regex_replace tool
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 20 Mar 2014 21:50:05 -0500 |
| parents | 9d5e59373c84 |
| children |
| rev | line source |
|---|---|
| 0 | 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. |
| 2 The workflow uses RSEM to quantify transcripts in an RNA-seq sample. | |
| 3 | |
| 4 See http://www.galaxyproject.org for information about the Galaxy Project. | |
| 5 | |
| 6 | |
| 7 Availability | |
| 8 ============ | |
| 9 | |
| 10 This workflow is available to download and/or install from the main | |
| 11 Galaxy Tool Shed: | |
| 12 | |
| 13 http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_reduced_db_workflow | |
| 14 | |
| 15 | |
| 16 Reference Data | |
| 17 ============== | |
| 18 | |
| 19 For Human RNAseq data this workflow was tested using reference data from: | |
| 20 | |
| 21 * ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.chromosome.[1-9XY]*.fa.gz | |
| 22 * ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz | |
| 23 * ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz | |
| 24 | |
| 25 | |
| 26 For Mouse RNAseq data this workflow was tested using reference data from: | |
| 27 | |
| 28 * ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.chromosome.[1-9XY]*.fa.gz | |
| 29 * ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz | |
| 30 * ftp://ftp.ensembl.org/pub/release-73/gtf/mus_musculus/Mus_musculus.GRCm38.73.gtf.gz | |
| 31 | |
| 32 | |
| 33 | |
| 34 Dependencies | |
| 35 ============ | |
| 36 | |
| 37 These dependencies should be resolved automatically via the Galaxy Tool Shed: | |
| 38 | |
| 39 * http://toolshed.g2.bx.psu.edu/view//jjohnson/rsem | |
| 40 * http://toolshed.g2.bx.psu.edu/view/devteam/fasta_formatter | |
| 41 | |
| 42 | |
| 43 History | |
| 44 ======= | |
| 45 | |
| 46 ======= ====================================================================== | |
| 47 Version Changes | |
| 48 ------- ---------------------------------------------------------------------- | |
| 49 v0.0.1 - Initial release to Tool Shed (March, 2014) | |
|
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20d9fb1ba210
Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
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50 v0.0.2 - Use regex_replace tool for tabular file manipulation |
| 0 | 51 ======= ====================================================================== |
| 52 | |
| 53 |