============================================================ CamoTSS for alternative TSS analysis in single cells

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Note

Hi there, my github account did not notify me when there are issue. So if you are in a hurry, you can email me. ruiyan@connect.hku.hk. I check email every day.

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/projects/CamoTSS/184603

Here, you can download some large file include genome.fa, possorted_genome_bam_filtered.bam.

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.

Note You should use the same reference gtf file and reference fasta file as that you used during alignment. In other words, if you run alignment by using cellranger, then the gtf file and fasta file should located in the refdata-gex-GRCh38-2020-A/fasta/genome.fa and refdata-gex-GRCh38-2020-A/genes/genes.gtf.

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, CC. & Huang, Y. CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data. Nat Commun 14, 7240 (2023). https://doi.org/10.1038/s41467-023-42636-1