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.

featureCounts 1.5.0-p1+dfsg-2                     January 2016                                  FEATURECOUNTS(1)