Easy upstream RNA-seq analysis for beginners
- The project should be used in Linux environment.
Prerequisites:
- A server/computer with fastqc, samtools, sratoolkit, hisat2. If you are using a server, you can use
module avil
to see if these required software are available. If not, please install it first or just find alternate ones.
How to use RNA-pipe:
- Install miniconda in your server.
- Change the working dictionary to RNA-pipe, and run
conda create -f rna-pipe.yml
- Change the file name in
rna-pipe.sh
to make sure it is proper for you.- Change the value of
PIPEDIR
to your folder where you have RNA-pipe. - Change the value of
SRADIR
if yourprefetch
fuction download it to other folder. Use the default value is OK. - Change the reference file place and file name in the step: # bulid index to the reference file you want. The default is used for the class.
- Change the value of
- Run
bash rna-pipe.sh
to get the results of count matrix.
This project is part of my work for the course bioinformatics at USTC. The default values are used for the samples of the class.