https://github.com/matteodelucchi/tr_cnv_in_expression_data
Pipeline to prepare RNA sequencing data for tandem repeat annotation with TRAL
https://github.com/matteodelucchi/tr_cnv_in_expression_data
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool cloud-computing
Last synced: about 1 month ago
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Pipeline to prepare RNA sequencing data for tandem repeat annotation with TRAL
- Host: GitHub
- URL: https://github.com/matteodelucchi/tr_cnv_in_expression_data
- Owner: matteodelucchi
- Created: 2019-06-10T16:10:17.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-07-07T11:03:58.000Z (almost 7 years ago)
- Last Synced: 2025-03-11T09:37:49.023Z (about 1 year ago)
- Topics: bioinformatics, bioinformatics-analysis, bioinformatics-pipeline, bioinformatics-scripts, bioinformatics-tool, cloud-computing
- Language: Shell
- Size: 1.01 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Tandem Repeat Copy Number Variation in \n Expression Data
This repository contains pipelines to preprocess RNAseq `.bam` files for the analysis with [TRAL](https://github.com/acg-team/tral).
## Setup and Installation of Dependencies
Download this repository
```bash
git clone https://github.com/matteodelucchi/TR_CNV_in_expression_data.git
```
Set up the directory struture for the files and install all necessary programs by sourcing the respective file for installation in a local environment or a high-performance cluster environment
```bash
chmod 779 setup_environment_cluster.sh
./setup_environment_cluster.sh
```
## Run Pipelines
The two proposed pipelines are provided in
* `reference-based_mapping_pipeline.sh`
* `de-novo_assembly.sh`
They are on early reasearch stage - don't run them as executables.
Go through each line very carefully step by step.