[](https://www.python.org/downloads/release/python-31015/)
[](https://www.python.org/downloads/release/python-31110/)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://github.com/astral-sh/ruff)
[](https://codecov.io/gh/janschleicher/tidesurf)
[](https://github.com/janschleicher/tidesurf/actions/workflows/python-package.yml)
# tidesurf
This repository provides a Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments using Python.
## Installation
Set up a virtual environment using Conda with Python version >=3.10 and activate it:
conda create -n <envName> python=3.10
conda activate <envName>
Clone the repository:
git clone git@github.com:janschleicher/tidesurf.git
Change into the directory and install with pip:
cd tidesurf
pip install -e .
## Usage
```
usage: tidesurf [-h] [-v] [--orientation {sense,antisense}] [-o OUTPUT]
[--filter_cells] [--whitelist WHITELIST | --num_umis NUM_UMIS]
[--min_intron_overlap MIN_INTRON_OVERLAP]
[--multi_mapped_reads]
SAMPLE_DIR GTF_FILE
Program: tidesurf (Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments)
Version: 0.1.dev31+g30b513e.d20241211
positional arguments:
SAMPLE_DIR Sample directory containing Cell Ranger output.
GTF_FILE GTF file with transcript information.
options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--orientation {sense,antisense}
Orientation of reads with respect to transcripts. For
10x Genomics, use 'sense' for three prime and
'antisense' for five prime.
-o OUTPUT, --output OUTPUT
Output directory.
--filter_cells Filter cells based on a whitelist.
--whitelist WHITELIST
Whitelist for cell filtering. Set to 'cellranger' to
use barcodes in the sample directory. Alternatively,
provide a path to a whitelist.
--num_umis NUM_UMIS Minimum number of UMIs for filtering a cell.
--min_intron_overlap MIN_INTRON_OVERLAP
Minimum number of bases that a read must overlap with
an intron to be considered intronic.
--multi_mapped_reads Take reads mapping to multiple genes into account
(default: reads mapping to more than one gene are
discarded).
```
## Contributing
For contributing, you should install `tidesurf` in development mode:
pip install -e ".[dev]"
This will install the additional dependencies `ruff` and `pytest`, which are used for formatting and code style, and testing, respectively.
Please run these before commiting new code.
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