bionic (1) featureCounts.1.gz

Provided by: subread_1.6.0+dfsg-1_amd64 bug

NAME

       featureCounts - a highly efficient and accurate read summarization program

SYNOPSIS

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

DESCRIPTION

       Version 1.6.0

       ## 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.

       -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_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 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.

       -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 bases included in a feature
              that  is required for overlapping with a read or a readpair. 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.

       --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>
              Perform strand-specific read counting. Acceptable values:  0  (unstranded),  1  (stranded)  and  2
              (reversely stranded).  0 by default.

       # Exon-exon junctions

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

       -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.

       # Miscellaneous

       -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.

       --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.