Hi dudes,

I want to count the number of my reads that have been mapped to each gene, then I downloaded featureCounts from http://sourceforge.net/projects/subread/files/subread-1.4.6-p5/, untarred that then using **my accepted_hits.sam** and **genes.gtf** as input, I replaced the command from documentation like below:

**Summarize a single-end read dataset using 5 threads**:

    featureCounts -T 5 -t exon -g gene_id -a annotation.gtf -o counts.txt mapping_results_SE.sam

```
[izadi@lbox161 Downloads]$ ls
subread-1.4.6-p5-source  subread-1.4.6-p5-source.tar.gz
[izadi@lbox161 Downloads]$ cd subread-1.4.6-p5-source
[izadi@lbox161 subread-1.4.6-p5-source]$ ls
LICENSE  README.txt  annotation  doc  ouput  src  test
[izadi@lbox161 subread-1.4.6-p5-source]$ cd src
[izadi@lbox161 src]$ ln -s /usr/data/nfs6/izadi/angel/ouput/
[izadi@lbox161 src]$ featureCounts -T 5 -t exon -g gene_id -a genes.gtf -o counts.txt accepted_hits.sam 
bash: featureCounts: command not found...
```

After untaring there no bin file there? do you know why?

    [izadi@lbox161 izadi]$ tar -zxvf subread-1.4.6-p5-source.tar.gz

May you please read my command and detect my fault here?

Thank you
Enter the src subdirectory under the home directory of the package and then issue the following command to build it on a Linux/unix computer:

    make -f Makefile.Linux

then the bin will be created and Enter that subdirectory under the home directory, now run your command

as simple as eating a piece of cake but not cheese one!