Repository htseq_count

Name: htseq_count

Owner: lparsons

Synopsis: Count aligned reads (SAM/BAM) that overlap genomic features (GFF)

Detailed description:

Uses the htseq-count script from the Python HTSeq package.

Given a file with aligned sequencing reads and a list of genomic features,
count how many reads map to each feature.

A feature is defined as an interval
(i.e., a range of positions) on a chromosome or a union of such intervals.

In the case of RNA-Seq, the features are typically genes, where each gene is defined
as the union of all it's exons. One may also consider each exon as a feature,
e.g., in order to check for alternative splicing. For comparative ChIP-Seq, the
features might be binding regions from a pre-determined list.

Content homepage: https://readthedocs.org/projects/htseq/

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count

Link to this repository: https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count/4418229c501e

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count

Type: unrestricted

Revision: 29:4418229c501e

This revision can be installed: True

Times cloned / installed: 7246

Repository README files - may contain important installation or license information

Readme files

htseq-count wrapper for Galaxy

Galaxy wrapper for htseq-count script from the HTSEQ python package.

Installation

Installation directly from the Galaxy Toolshed is recommended.

Galaxy Wrapper License

Licensed under the BSD 2-Clause License: <http://opensource.org/licenses/BSD-2-Clause>

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.