subread的下载和使用

subread依赖zlib，应先配置编译环境，安装相关依赖包。
（https://www.huaweicloud.com/kunpeng/software/Subread.html）

yum install -y zlib-devel

wget -c https://sourceforge.net/projects/subread/files/subread-2.0.0/subread-2.0.0-Linux-x86_64.tar.gz

tar zxvf subread-2.0.0-Linux-x86_64.tar.gz

还需要下载 [subread-2.0.0-source.tar.gz](https://sourceforge.net/projects/subread/files/subread-2.0.0/subread-2.0.0-source.tar.gz/download)

wget -c https://sourceforge.net/projects/subread/files/subread-2.0.0/subread-2.0.0-source.tar.gz/download

进入 [subread-2.0.0-source.tar.gz](https://sourceforge.net/projects/subread/files/subread-2.0.0/subread-2.0.0-source.tar.gz/download)的src文件夹

make -f Makefile.Linux

PS: 如果编译失败, 如下:

(base) lchen@Vostro-5460:~/biosoft/subread-2.0.0-source/src$ make -f Makefile.Linux

gcc  -mtune=core2  -O3 -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64    -fmessage-length=0  -ggdb    -c -o core.o core.c

In file included from core.c:45:0:

subread.h:26:10: fatal error: zlib.h: 没有那个文件或目录

#include 

          ^~~~~~~~

compilation terminated.

<内置>: recipe for target 'core.o' failed

make: *** [core.o] Error 1

可能是zlib没下载好,Ubuntu用户可用下句来修复

参考: rico-yang

sudo apt-get install zlib1g-dev

继续完成编译

make -f Makefile.Linux

××ubuntu or debian：

安装zlib包并不是apt-get install zlib

而是用

apt-get install zlib1g-dev

此提示为缺少库文件，安装即可××，ubuntu下安装方法：

sudo apt-get install zlib1g-dev libssl-dev
![image.png](https://upload-images.jianshu.io/upload_images/19998777-a341a3c9237a1ca4.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240)

设置环境变量：

将“export PATH=/mnt/d/workplace/biosoft/subread-2.0.1-source/bin:$PATH”写入“/etc/profile”文件最后一行。

nano /etc/profile
export PATH=/mnt/d/workplace/biosoft/subread-2.0.1-source/bin:$PATH

source /etc/profile

运行和验证

查看Subread版本:
subread-align -v
回显如下信息则表示Subread安装成功:
Subread-align v2.0.1

使用

reads比对到参考基因组

第一步：构建索引

subread要求参考基因组的fasta必须要构建索引

subread-buildindex -o hg38 hg38.fa

实例

subread-buildindex -o ~/reference/subread_index/hg38 ~/reference/index/hg38.fa