dge_howto.md 1.32 KB
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[TOC]: # " RNA Seq workflow tutorial"
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# RNA Seq workflow tutorial
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- [Project Setup](#project-setup)
- [RNA-Seq with DESeq2](#rna-seq-with-deseq2)
- [Differential expression with limma](#differential-expression-with-limma)
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Project Setup
-------------
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1. Create new git repo under `git.mpi-cbg.de`
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2. Clone repo to cluster `scripts/${PRJ_NAME}`
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3. Create project directory under `/projects/bioinfo/data/${PRJ_NAME}`
4. Create `README.md` in repo and populate with project info
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5. Check quota with `quotalist` for enough space (rule of thumb 10gb per sample)
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Differential expression with DESeq2
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-------------------
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1. Copy template `dge_workflow/dge_star_template.sh` into project repo
2. Adjust template properties and run `featcounts_deseq_mf.R`.
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Differential expression with limma
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Prepare `design`, `contrasts` and `expression/abundance matrix` as for DESeq2 workflow and run

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```bash
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## basic usage
rend.R --toc ${NGS_TOOLS}/dge_workflow/limma/dge_limma.R  inten_matrix_acc.txt exp_design.txt

## with more optional arguments
rend.R --toc ${NGS_TOOLS}/dge_workflow/limma/dge_limma.R --gene_info mmus_ens_aug2017_uniprot_compl_gene_info.txt --contrasts example_contrasts.txt inten_matrix_acc.txt exp_design.txt

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```

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For a complete list of arguments
see `${NGS_TOOLS}/dge_workflow/limma/dge_limma.R --help`