featureCounts is a highly efficient and accurate read summarization program.
The general syntax of the command is:
featureCounts [options] -a [annotation_file] -o [output_file] input_file1 [input_file2]
In case if you encounter below error:
featureCounts: command not found
You may need to install the subread package according to your choice of operating system:
| Distribution | Command |
|---|---|
| Debian | apt-get install subread |
| Ubuntu | apt-get install subread |
| Kali Linux | apt-get install subread |
| Raspbian | apt-get install subread |
The Subread package comprises a suite of software programs for processing next-gen sequencing read data including:
- Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
- featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
- Sublong: a long-read aligner that is designed based on seed-and-vote.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.