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featureCounts: command not found

by admin

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.

Filed Under: Linux

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