.. _promoter-identification:

Promoter Identification
=======================

Documentation and scripts for identifying alternative promoter usage (APU) by 
integrating multi-omics datasets.

.. _reports-notebooks:

Reports & Notebooks
-------------------

.. toctree::
   :maxdepth: 1

   scripts/1_promoter_identification/1A_integration_pacbiotss_proactiv_published_only
   scripts/1_promoter_identification/1B_identify_targetregion_dualguides
   scripts/1_promoter_identification/1C_refTSS_andTSS

Overview
--------

This section contains three main analyses for identifying and characterizing alternative promoters:

* **1A: Integration Analysis** - Combines PacBio long-read data, CAGE-seq TSS data, and proActiv predictions
* **1B: Target Region Identification** - Defines optimal regions for dual guide targeting
* **1C: RefTSS Comparison** - Validates identified promoters against reference annotations

**Quick Downloads:**

* :download:`1A Integration Report (HTML) <scripts/1_promoter_identification/1A_integration_pacbiotss_proactiv_published_only.html>`
* :download:`1B Target Region Report (HTML) <scripts/1_promoter_identification/1B_identify_targetregion_dualguides.html>`
* :download:`1C refTSS Comparison (HTML) <scripts/1_promoter_identification/1C_refTSS_andTSS.html>`