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.