.. _home-page-moptail:

*******************
MOP_TAIL
*******************

.. autosummary::
   :toctree: generated

This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files, alignment and assignment read ID to gene/transcript. It outputs the estimation of poly(A) tail length at read level provided by **Tailfindr**, **Nanopolish** or both. Tailfinr can be run using three modes: standard, for Nano3P-seq protocol with R9 chemistry and Nano3P-seq protocol with R10 chemistry.

.. image:: ../img/flow_tail.png
  :width: 600
  :alt: mop_tail graph


Input Parameters
======================

The input parameters are stored in yaml files like the one represented here:

.. literalinclude:: ../mop_tail/params.yaml
   :language: yaml



How to run the pipeline
=============================
Before launching the pipeline,user should:

1. Decide which containers to use - either docker or singularity **[-with-docker / -with-singularity]**.
2. Fill in both **params.config** and **tools_opt.tsv** files.

To launch the pipeline, please use the following command:

.. code-block:: console

   nextflow run mop_tail.nf -params-file params.yaml  -with-singularity > log.txt


You can run the pipeline in the background adding the nextflow parameter **-bg**:

.. code-block:: console

   nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg > log.txt

You can change the parameters either by changing **params.config** file or by feeding the parameters via command line:

.. code-block:: console

   nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt


You can specify a different working directory with temporary files:

.. code-block:: console

   nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt


Results
====================

Several folders are created by the pipeline within the output directory specified by the **output** parameter:

1. NanoPolish: contains the output of *nanopolish* tool.
2. Tailfindr: contains the output of *tailfindr* tool.
3. PolyA_final: contains the txt files with the combined results (i.e. predicted polyA sizes). Here an example of a test:

.. code-block:: console

   "Read name"	"Tailfindr"	"Nanopolish"	"Gene Name"
   "013a5dde-9c52-4de1-83eb-db70fb2cd130"	52.16	49.39	"YKR072C"
   "01119f62-ca68-458d-aa1f-cf8c8c04cd3b"	231.64	274.28	"YDR133C"
   "0154ce9c-fe6b-4ebc-bbb1-517fdc524207"	24.05	24.24	"YFL044C"
   "020cde28-970d-4710-90a5-977e4b4bbc46"	41.27	56.79	"YGL238W"

If both programs are run, an additional plot that shows the correlation of their results is generated.

.. image:: ../img/mod_corr.png
  :width: 400