(My CodeOcean) Calling Feature Counts Matrix from RNA-seq Fastq sequence data

Date: Nov. 3, 2020
After well-thought, if you have any question, plz sent E-mail to me. I will back you in 24 hours
 
please contact with me via the following ways:
(a) e-mail :yuansh3354@163.com
(b) QQ : 1044532817
 
Best Regards,
Yuan Sh, MD (ORCID: 0000-0002-6028-0185)
Github: https://github.com/yuansh3354
¹Fujian Medical University. No. 1 Xue Yuan Road,University Town, 350122 FuZhou Fujian, China
²National Center for Nanoscience and Technology (NCNST). No.11 ZhongGuanCun BeiYiTiao, 100190 Beijing, China

配置基础conda 环境

# 储存空间太大，可以随意挥霍
# 一个项目一个环境
conda create --name WQ-RNA --clone base
conda activate WQ-RNA

# 安装软件
conda install -y star
conda install -y trimmomatic
conda install -y cutadapt
conda install -y trim-galore
conda install -y hisat2 
conda install -y fastqc 
conda install -y multiqc 
conda install -y samtools 
conda install -y featureCounts

设置基础环境变量

wkd= # 设置自己的工作目录
rawdata=$wkd/rawdata # 原始数据存放地址
hista2_index= *** # 参考基因组
gtf= *** # GTF 文件
Matrix_name= ** # 输出的矩阵名字

质量控制

echo "First fastqc is processing ..."
echo "First fastqc starts at `date`"

fastq=