Provided by: subread_1.5.0-p1+dfsg-2_amd64 
NAME
featureCounts - a highly efficient and accurate read summarization program
USAGE
featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2] ...
Required arguments:
-a <string>
Name of an annotation file. GTF 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' and `SAF'. `GTF' 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 Count fragments (read pairs) instead of individual reads. For each read pair, its two reads must
be adjacent to each other in BAM/SAM input.
-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.
-S <ff:fr:rf>
Specify orientation of two reads from the same pair, 'fr' by by default (forward/reverse).
-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.