.. _geneset_overlap:

Step 3 - map gene/transcript IDs
================================

To be able to link gene ages assignments from an orthomap and gene or transcript
of scRNA dataset, one needs to check the overlap of the annotated gene names.

With the `gtf2t2g` submodule of `oggmap` and the `gtf2t2g.parse_gtf()`
function, one can extract gene and transcript names from a given gene feature
file.

How to match gene or transcript IDs between an orthomap and scRNA data
----------------------------------------------------------------------

Please download the notebooks from `here <https://raw.githubusercontent.com/kullrich/oggmap/main/docs/notebooks/geneset_overlap.ipynb>`_
or please click below to view the content.

.. toctree::

   ../notebooks/geneset_overlap