https://github.com/likelet/rnaseqpipe

Nextflow based RNA-seq analysis pipeline
https://github.com/likelet/rnaseqpipe

Last synced: 28 days ago
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Nextflow based RNA-seq analysis pipeline

• Host: GitHub
• URL: https://github.com/likelet/rnaseqpipe
• Owner: likelet
• Created: 2018-08-17T03:11:19.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2021-11-19T08:13:13.000Z (over 3 years ago)
• Last Synced: 2025-04-22T00:18:49.073Z (about 1 month ago)
• Language: Perl
• Homepage:
• Size: 131 KB
• Stars: 3
• Watchers: 2
• Forks: 6
• Open Issues: 0
• Metadata Files:
  • Readme: Readme.md

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README

        
# SYSUCC-RNAseqPipe

### Quick start  for reproductive analysis 

    nextflow run RNAseqPipe/main.nf -profile c2 --read "*_{1,2}.fq.gz" --designfile "design.file" --comparefile "compare.txt"

### Documentation

The SYSUCC-RNAseqPipe pipeline comes with documentation about the pipeline, found in the `docs/` directory:  

please find the information in [wiki](https://github.com/likelet/RNAseqPipe/wiki)  

1. [Installation and configuration](docs/Installation.md)

2. [Running the pipeline](docs/usage.md)

3. [Output and how to interpret the results](docs/output.md)

### Dependencies 

* Softwares 

    * [fastp](https://github.com/OpenGene/fastp)

    * [STAR](https://github.com/alexdobin/STAR)

    * [RSEM](https://deweylab.github.io/RSEM/)

    * [Qualimap](http://qualimap.bioinfo.cipf.es/)

    * [DAtools](https://github.com/likelet/DAtools)

    * [MultiQC](https://github.com/ewels/MultiQC)

    * [GSEA](http://software.broadinstitute.org/gsea/index.jsp)  

    * Several R packages for downstream analysis.

### Input file  

* `design.txt`  

sampleInfor presents the experimental design of your data set, it is just like a design file of `DESeq2` and `EdgeR` input.  

        Sample	Type

        P1003NA	N

        P1003TA	T

        P1162NA	N

        P1162TA	T

        P1408NA	N

        P1408TA	T

        P1527NA	N

        

* `compare.txt`

specify which group to compare in your differential expression analysis 

        

        T_vs_N

       

`T` and `N` are the identical strings as the `Type` column in `design.txt`.

### command parameters 

* `--reads`  

    

    suffix of your raw reads file. For example, `*_{1,2}.fq.gz` for paired end reads file `sampleA_1.fq.gz` and `sampleA_2.fq.gz `  

    

* `--designfile`  

    

    design file  

    

* `--comparefile`  

    

    compare file 

    

* `--gene_gtf`  

    

    gtf file for building your STAR index 

* `--singleEnd`  

    

    `true` when using a single End reads input, default `false` 

* `--strand`  

    

    `true` when using strand specific library , default `false` 

     

* `--skip_qc`   

    set `ture` if you are going to skip qc step 

    

* `--without_replicate`   

    set `ture` if your have no biological replicate.       

    *note: for no replicate mode, the compare file should be directly specified as `SampleName_vs_SampleName` have just been trimmed by `read` suffix string *  

    

# Credits 

* Main author:

  * Qi Zhao ([@qi_likelet](https://github.com/likelet/))

* Contributors:

  * Xiaolong Zhang

  * Kaiyu