RNA-pipe

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:

1. Install miniconda in your server.
2. Change the working dictionary to RNA-pipe, and run conda create -f rna-pipe.yml
3. Change the file name in rna-pipe.sh to make sure it is proper for you.
   1. Change the value of PIPEDIR to your folder where you have RNA-pipe.
   2. Change the value of SRADIR if your prefetch fuction download it to other folder. Use the default value is OK.
   3. 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.
4. 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.