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Update run_on_sumner.md
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lmurba authored Apr 20, 2021
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Expand Up @@ -89,6 +89,8 @@ If you already created a `NF_splicing_pipeline.config` during the trim test, you

- To run full pipeline, you **must** specify the following: `reads.csv`, `rmats_pairs.txt`, `readlength`, `assembly_name`, `star_index`, and `reference gtf`. This string can be a relative path from the directory in which you run Nextflow in, an absolute path or a link.

- Currently, the two options for genomes are hg38 and mm10. If you wish to use a newer version of the genome, you will need to add this to the post-processing script

### 5. Run the pipeline!

Ensure you have `NF_splicing_pipeline.config` in this directory.
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