By default, HTSeq has a count script for doing either paired ends or single end reads. MixedHTSeq extends this to cover cases where you have a mixture of the two due to QC tools like AdapterRemoval.
MixedHTSeq can be installed using the following commands (on linux machines)
git clone https://github.com/schae234/MixedHTSeq.git
cd MixedHTSeq
pip install numpy pandas
python setup.py install
Note: MixedHTSeq requires python2.7 and numpy
MixedHTSeq comes with several scripts which are in the scripts/ directory.
cd scripts/
python mixed_count.py --help
See original Docs here
MixedHTSeq and HTSeq are free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
The full text of the GNU General Public License, version 3, can be found here: http://www.gnu.org/licenses/gpl-3.0-standalone.html