CamoTSS 0.1.5

CamoTSS: Detection alternative TSS in single cells

Installation

You can install from this GitHub repository for latest (often development) version by following command line

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.

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 two modes in CamoTSS : TC and CTSS.

You can run CamoTSS by using test file according to the following code.

#!/bin/bash
gtfFile= $CamoTSS/test/Homo_sapiens.GRCh38.105.chr_test.gtf
fastaFile = $download/genome.fa
bamFile= $download/possorted_genome_bam_filtered.bam
cellbarcodeFile=$CamoTSS/test/cellbarcode_to_CamoTSS

CamoTSS --gtf gtfFile --refFasta fastaFile --bam bamFile -c cellbarcodeFile -o CamoTSS_out --mode TC

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.

Detailed Manual

The full manual is here, including:

Preprocess

Run CamoTSS

Detect alternative TSS/CTSS

Reference

Coming soon