============================================================
CamoTSS for alternative TSS analysis in single cells
============================================================
|pypi|
.. |pypi| image:: https://badge.fury.io/py/CamoTSS.svg
:target: https://pypi.org/project/CamoTSS/
Installation
============
You can install from this GitHub repository for latest (often development)
version by following command line
.. code-block:: bash
pip install -U git+https://github.com/StatBiomed/CamoTSS
In either case, add ``--user`` if you don't have the write permission for your
Python environment.
Quick start
===========
Download test file
===================
You can download test file from figshare_.
.. _figshare: https://figshare.com/articles/dataset/CamoTSS_test_data/22641031
Here, you can download some large file include genome.fa, possorted_genome_bam_filtered.bam.
Alternatively, you can also download the reference genome fasta file from Ensembl or Genecode or website of 10x Genomics.
Run CamoTSS
=============
Here are three modes in CamoTSS : **TC+CTSS** , **TC** and **CTSS**.
When you run **TC+CTSS** mode, you will get TC result and then get the CTSS result based on the TC.
When you run **TC** mode, you will only get the TC result.
The **TC+CTSS** and **TC** mode have the same required files.
The --outdir is the only required parameter for **CTSS** mode. But the outdir should include output of TC.
If you want to run **CTSS** mode, you must based on the output of TC.
You can run CamoTSS **TC+CTSS** mode by using test file according to the following code.
For the remaining modes, you can check this document_.
.. _document: https://camotss.readthedocs.io/en/latest/run_CamoTSS.html
.. code-block:: bash
#!/bin/bash
gtfFile= $download/Homo_sapiens.GRCh38.105.chr_test.gtf
fastaFile = $download/genome.fa
bamFile= $download/possorted_genome_bam_filtered.bam
cellbarcodeFile=$download/cellbarcode_to_CamoTSS
CamoTSS --gtf gtfFile --refFasta fastaFile --bam bamFile -c cellbarcodeFile -o CamoTSS_out --mode TC+CTSS
Alternative TSS or CTSS detecting
=================================
To identify alternative TSS usage or alternative CTSS usage, Brie2 (Huang & Sanguinetti, 2021) is recommend to be used.
Here, we provide an example exploiting BRIE2 to detect alterntive TSS/CTSS usage.
You can check it in our manual_.
.. _manual: https://camotss.readthedocs.io/en/latest/runBRIE.html
Detailed Manual
================
The full manual is here_, including:
`Preprocess`_
`Run CamoTSS`_
`Detect alternative TSS/CTSS`_
.. _here: https://camotss.readthedocs.io/en/latest/index.html
.. _Preprocess: https://camotss.readthedocs.io/en/latest/preprocess.html
.. _Run CamoTSS: https://camotss.readthedocs.io/en/latest/run_CamoTSS.html
.. _Detect alternative TSS/CTSS: https://camotss.readthedocs.io/en/latest/runBRIE.html
Reference
===========
Hou, R., Hon, C. C., & Huang, Y. (2023). CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5'scRNA-seq data. bioRxiv, 2023-04.
Raw data
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