USAGE

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')

input_files

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.

-f

Perform read counting at feature level (eg. counting reads for exons rather than genes).

-O

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.

-M

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.

-v

Output version of the program.

-J

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.

-R

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.

--largestOverlap

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.

--fraction

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.

--primary

Count primary alignments only. Primary alignments are identified using bit 0x100 in SAM/BAM FLAG field.

--ignoreDup

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.

-p

If specified, fragments (or templates) will be counted instead of reads. This option is only applicable for paired-end reads.

-P

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.

-B

Count read pairs that have both ends successfully aligned only.

-C

Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.

--donotsort

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.