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

1. Installation and configuration
2. Running the pipeline
3. Output and how to interpret the results

Dependencies

• Softwares
  • fastp
  • STAR
  • RSEM
  • Qualimap
  • DAtools
  • MultiQC
  • GSEA
  • 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)
• Contributors:
  • Xiaolong Zhang
  • Kaiyu