pysplicing's Introduction

TACOS

Trichomonad Assembler for COmplex Splicing

TACOS pipeline is divided into three main steps:

1.- RNAseq mapping to the reference genome.
2.- Processing of the SJs.
3.- Transcript assembly

The complete pseudo-code can be summaryzed as follows:

Installation

Before running TACOS, please make sure you meet the following requirements:

TACOS has been tested on python 3.8.12, and needs the following libraries/software (some might require manual installation):

import tabulate
import plotext
import pysam
import six

STAR
StringTie
Samtools

Running TACOS

1. Mapping

Mapping parameters. TACOS has been tested with STAR 2.7.6a. Custom parameters for mapping are not needed (nor reccomended), however the use of the following parameters is mandatory:

--outSAMtype BAM SortedByCoordinate 
--outSAMstrandField intronMotif 
--outSAMattributes All

BAM file must be indexed, and the index must be present in the same path. It can be obtained with samtools by running:

samtools index file.bam

2. Running the main script

python tacos_v2.py -h 

usage: tacos_v2.py [-h] -f INPUT -sj SJ_STAR -b BAM_F -o OUTPUT -5m MOTIF5P -3m MOTIF3P

Trichomonad assembler for complex splicing
---------------------
Tested on python 3.8.12

optional arguments:
  -h, --help            show this help message and exit

Mandatory arguments:
  -f INPUT, --input, Input fasta file (Genome reference)
                        
  -sj SJ_STAR, --input_sj, SJ.out.tab from STAR mapping
                        
  -b BAM_F, --input_bam, BAM file from STAR mapping
                        
  -o OUTPUT, --output, Prefix: Prefix for output files
                        
  -5m MOTIF5P, --5p-motif, String: Splicing motif at 5p (upper case nucleotides only, no spaces)
                        
  -3m MOTIF3P, --3p-motif, String: Splicing motif at 3p (upper case nucleotides only, no spaces)