featureCounts(1) a highly efficient and accurate read summarization program


featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2] ...

Required arguments:

-a <string>
Name of an annotation file. GTF/GFF format by default. See -F option for more formats.
-o <string>
Name of the output file including read counts. A separate file including summary statistics of counting results is also included in the output (`<string>.summary')
List of input files in BAM or SAM format. Users do not need to specify it is BAM or SAM.

Optional arguments:

-A <string>
Name of a comma delimited file including chromosome alias names used to match chromosome names used in annotation with those used in BAM/SAM input, if they are different. See Users Guide for file format.
-F <string>
Specify format of provided annotation file. Acceptable formats include `GTF/GFF' and `SAF'. `GTF/GFF' by default. See Users Guide for description of SAF format.
-t <string>
Specify feature type in GTF annotation. `exon' by default. Features used for read counting will be extracted from annotation using the provided value.
-g <string>
Specify attribute type in GTF annotation. `gene_id' by default. Meta-features used for read counting will be extracted from annotation using the provided value.
Perform read counting at feature level (eg. counting reads for exons rather than genes).
Assign reads to all their overlapping meta-features (or features if -f is specified).
-s <int>
Perform strand-specific read counting. Possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.
Multi-mapping reads will also be counted. For a multimapping read, all its reported alignments will be counted. The `NH' tag in BAM/SAM input is used to detect multi-mapping reads.
-Q <int>
The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default.
-T <int>
Number of the threads. 1 by default.
Output version of the program.
Count number of reads supporting each exon-exon junction. Junctions were identified from those exon-spanning reads in the input (containing 'N' in CIGAR string). Counting results are saved to a file named '<output_file>.jcounts'
-G <string>
The Fasta file containing the reference genome used in generating the input SAM or BAM files. This argument is only needed when doing junction counting.
Output detailed assignment result for each read. A text file will be generated for each input file, including names of reads and meta-features/features reads were assigned to. See Users Guide for more details.
Assign reads to a meta-feature/feature that has the largest number of overlapping bases.
--minOverlap <int>
Specify minimum number of overlapping bases required between a read and a meta-feature/feature that the read is assigned to. 1 by default.
--read2pos <5:3>
Reduce reads to their 5' most base or 3' most base. Read counting is then performed based on the single base the read is reduced to.
--readExtension5 <int> Reads are extended upstream by <int> bases from their
5' end.
--readExtension3 <int> Reads are extended upstream by <int> bases from their
3' end.
Use a fractional count 1/n, instead of 1 (one) count, for each reported alignment of a multi-mapping read in read counting. n is total number of alignments reported for the multi-mapping read. This option must be used together with '-M' option.
Count primary alignments only. Primary alignments are identified using bit 0x100 in SAM/BAM FLAG field.
Ignore duplicate reads in read counting. Duplicate reads are identified using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one of the reads is a duplicate read for paired end data.
--countSplitAlignmentsOnly Count split alignments only (ie. alignments with
CIGAR string containing `N'). An example of split alignments is exon-spanning reads in RNA-seq data.
If specified, fragments (or templates) will be counted instead of reads. This option is only applicable for paired-end reads.
Check validity of paired-end distance when counting read pairs. Use -d and -D to set thresholds.
-d <int>
Minimum fragment/template length, 50 by default.
-D <int>
Maximum fragment/template length, 600 by default.
Count read pairs that have both ends successfully aligned only.
Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.
Do not sort reads in BAM/SAM input. Note that reads from the same pair are required to be located next to each other in the input.
--maxMOp <int>
Maximum number of 'M' operations allowed in a CIGAR string . 10 by default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations are merged in the CIGAR string.