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General Description

HTSeq version 0.6.1

Basic Usage

module load bio #to load all bio modules
module load bio/htseq/0.6.1 #to load htseq alone 

Useful Options

Usage: htseq-count [options] alignment_file gff_file

This script takes an alignment file in SAM/BAM format and a feature file in
GFF format and calculates for each feature the number of reads mapping to it.
See for details.

  -h, --help            show this help message and exit
  -f SAMTYPE, --format=SAMTYPE
                        type of <alignment_file> data, either 'sam' or 'bam'
                        (default: sam)
  -r ORDER, --order=ORDER
                        'pos' or 'name'. Sorting order of <alignment_file>
                        (default: name). Paired-end sequencing data must be
                        sorted either by position or by read name, and the
                        sorting order must be specified. Ignored for single-
                        end data.
  -s STRANDED, --stranded=STRANDED
                        whether the data is from a strand-specific assay.
                        Specify 'yes', 'no', or 'reverse' (default: yes).
                        'reverse' means 'yes' with reversed strand
  -a MINAQUAL, --minaqual=MINAQUAL
                        skip all reads with alignment quality lower than the
                        given minimum value (default: 10)
                        feature type (3rd column in GFF file) to be used, all
                        features of other type are ignored (default, suitable
                        for Ensembl GTF files: exon)
  -i IDATTR, --idattr=IDATTR
                        GFF attribute to be used as feature ID (default,
                        suitable for Ensembl GTF files: gene_id)
  -m MODE, --mode=MODE  mode to handle reads overlapping more than one feature
                        (choices: union, intersection-strict, intersection-
                        nonempty; default: union)
  -o SAMOUT, --samout=SAMOUT
                        write out all SAM alignment records into an output SAM
                        file called SAMOUT, annotating each line with its
                        feature assignment (as an optional field with tag
  -q, --quiet           suppress progress report

Written by Simon Anders (, European Molecular Biology
Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
Public License v3. Part of the 'HTSeq' framework, version 0.6.0.

Further Information

See the official website: [http:// ]