Provided by: subread_2.0.4+dfsg-1_amd64 bug

NAME

       featureCounts - toolkit for processing next-gen sequencing data

SYNOPSIS

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

DESCRIPTION

       Version 2.0.4

       ## Mandatory arguments:

       -a <string>
              Name of an annotation file. GTF/GFF format by  default.  See  -F  option  for  more
              format  information.  Inbuilt annotations (SAF format) is available in 'annotation'
              directory of the package. Gzipped file is also accepted.

       -o <string>
              Name of output file including  read  counts.  A  separate  file  including  summary
              statistics of counting results is also included in the output ('<string>.summary').
              Both files are in tab delimited format.

       input_file1 [input_file2] ...
              A list of SAM or BAM format files. They can be

       either name or location sorted. If no files provided,
              <stdin> input is  expected.  Location-sorted  paired-end  reads  are  automatically
              sorted by read names.

       ## Optional arguments: # Annotation

       -F <string>
              Specify  format  of  the provided annotation file. Acceptable formats include 'GTF'
              (or compatible GFF format) and 'SAF'. 'GTF' by default.   For  SAF  format,  please
              refer to Users Guide.

       -t <string>
              Specify  feature  type(s) in a GTF annotation. If multiple types are provided, they
              should be separated by ',' with no space in between. 'exon' by default. Rows in the
              annotation with a matched feature will be extracted and used for read mapping.

       -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.

       --extraAttributes
              Extract extra attribute types from the provided GTF annotation and include them  in
              the  counting  output. These attribute types will not be used to group features. If
              more than one attribute type is provided they should be separated by comma.

       -A <string>
              Provide a chromosome name alias file to match chr names in annotation with those in
              the  reads.  This should be a twocolumn comma-delimited text file. Its first column
              should include chr names in the annotation and its second column should include chr
              names  in  the  reads.  Chr  names  are  case sensitive. No column header should be
              included in the file.

       # Level of summarization

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

       # Overlap between reads and features

       -O     Assign  reads  to  all  their  overlapping  meta-features  (or  features  if  -f is
              specified).

       --minOverlap <int>
              Minimum number of overlapping bases in a read that is required for read assignment.
              1 by default. Number of overlapping bases is counted from both reads if paired end.
              If a negative value is provided, then a gap of up to specified size will be allowed
              between read and the feature that the read is assigned to.

       --fracOverlap <float> Minimum fraction of overlapping bases in a read that is
              required  for  read  assignment.  Value should be within range [0,1]. 0 by default.
              Number of overlapping bases is counted from both reads if  paired  end.  Both  this
              option and '--minOverlap' option need to be satisfied for read assignment.

       --fracOverlapFeature <float> Minimum fraction of overlapping bases in a
              feature that is required for read assignment. Value should be within range [0,1]. 0
              by default.

       --largestOverlap
              Assign reads to a meta-feature/feature that has the largest number  of  overlapping
              bases.

       --nonOverlap <int>
              Maximum  number of non-overlapping bases in a read (or a read pair) that is allowed
              when being assigned to a feature. No limit is set by default.

       --nonOverlapFeature <int> Maximum number of non-overlapping bases in a feature
              that is allowed in read assignment. No limit is set by default.

       --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.

       --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.

       # Multi-mapping reads

       -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.

       # Fractional counting

       --fraction
              Assign  fractional  counts to features. This option must be used together with '-M'
              or  '-O'  or  both.  When  '-M'  is  specified,  each  reported  alignment  from  a
              multi-mapping  read (identified via 'NH' tag) will carry a fractional count of 1/x,
              instead of 1 (one), where x is the total number of alignments reported for the same
              read.  When  '-O'  is specified, each overlapping feature will receive a fractional
              count of 1/y, where y is the total number of features overlapping  with  the  read.
              When both '-M' and '-O' are specified, each alignment will carry a fractional count
              of 1/(x*y).

       # Read filtering

       -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.

       --splitOnly
              Count  split  alignments only (ie. alignments with CIGAR string containing 'N'). An
              example of split alignments is exon-spanning reads in RNA-seq data.

       --nonSplitOnly
              If specified, only non-split alignments (CIGAR strings do not contain  letter  'N')
              will be counted. All the other alignments will be ignored.

       --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.

       # Strandness

       -s <int or string>
              Perform strand-specific read counting. A single integer value (applied to all input
              files)  or  a  string of commaseparated values (applied to each corresponding input
              file) should be provided. Possible values include: 0 (unstranded), 1 (stranded) and
              2  (reversely  stranded).  Default value is 0 (ie. unstranded read counting carried
              out for all input files).

       # Exon-exon junctions

       -J     Count  number  of  reads  supporting  each  exon-exon  junction.   Junctions   were
              identified  from  all the exon-spanning reads in the input (containing 'N' in CIGAR
              string). Counting results are saved to a file named '<output_file>.jcounts'

       -G <string>
              Provide the name of a FASTA-format file that contains the reference sequences  used
              in  read  mapping  that produced the provided SAM/BAM files. This optional argument
              can be used with '-J' option to improve read counting for junctions.

       # Parameters specific to paired end reads

       -p     If specified, libraries are assumed to contain paired-end reads.  For  any  library
              that  contains  paired-end  reads,  the 'countReadPairs' parameter controls if read
              pairs or reads should be counted.

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

       -B     Only count read pairs that have both ends aligned.

       -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.

       -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.

       # Number of CPU threads

       -T <int>
              Number of the threads. 1 by default.

       # Read groups

       --byReadGroup
              Assign reads by read group. "RG" tag is required to be present in the input BAM/SAM
              files.

       # Long reads

       -L     Count long reads such as Nanopore and PacBio reads. Long read counting can only run
              in one thread and  only  reads  (not  read-pairs)  can  be  counted.  There  is  no
              limitation  on  the number of 'M' operations allowed in a CIGAR string in long read
              counting.

       # Assignment results for each read

       -R <format>
              Output detailed assignment results for each read or readpair. Results are saved  to
              a  file that is in one of the following formats: CORE, SAM and BAM. See Users Guide
              for more info about these formats.

       --Rpath <string>
              Specify a directory to save the detailed assignment results.  If  unspecified,  the
              directory where counting results are saved is used.

       # Miscellaneous

       --tmpDir <string>
              Directory  under  which  intermediate  files are saved (later removed). By default,
              intermediate files will be saved to the directory specified in '-o' argument.

       --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.

       --verbose
              Output verbose information  for  debugging,  such  as  unmatched  chromosome/contig
              names.

       -v     Output version of the program.

AUTHOR

        This manpage was written by Alexandre Mestiashvili for the Debian distribution and
        can be used for any other usage of the program.