RNA_seq_analysis_pipe

This is for the QC matrix construction, data analysis and visualization for RNA-seq data.
Current version: v4

Advisor: Bo Zhang
Contributor: Cheng Lyu and Shaopeng Liu

For any question, please contact Wustl.Zhanglab@gmail.com

Usage:

Singularity 2-step solution (easiest way)

Step1. download singularity container (you only need download the containcer for once, then you can use them directly):

# download image from local server:  
wget http://regmedsrv1.wustl.edu/Public_SPACE/shaopengliu/Singularity_image/rna-seq/rna-seq_mm10_v4.simg  

or for human

# download image from local server:
wget http://regmedsrv1.wustl.edu/Public_SPACE/shaopengliu/Singularity_image/rna-seq/hg38_rna-seq.simg

Step2. process data by the singularity image:

Please run at same directory with your data OR the soft link of your data

singularity run -H ./:/scratch rna-seq_mm10_v4.simg -r <SE/PE> -g <mm10>  -o <read_file1>  -p <read_file2>    

That's it!

#parameters:
-h: help information
-r: SE for single-end, PE for paired-end
-g: genome reference, one simg is designed for ONLY one species due to the file size. For now the supported genoms are: <mm10/mm9/hg19/hg38/danRer10> (only mm10 in the example).
-o: reads file 1 or the SE reads file, must be ended by .fastq or .fastq.gz or .sra (for both SE and PE)
-p: reads file 2 if input PE data, must be ended by .fastq or .fastq.gz
-a: ADAPT1 for cutadapt
-b: ADAPT2 for cutadapt, if not specified there will be ONLY quality trimming rather than adapter trimming
-t: (optional) specify number of threads to use, default 24

e.g: a) mm10 SE data A.fastq

singularity run -H ./:/scratch <path_to_simg>  -r SE -g mm10 -o A.fastq  

b) hg38 PE data B_1.fastq B_2.fastq

singularity run -H ./:/scratch <path_to_simg>  -r PE -g hg38 -o B_1.fastq  -p B_2.fastq  

c) danRer10 PE data in sra file C.sra

singularity run -H ./:/scratch <path_to_simg> -r PE -g danRer10 -o C.sra