XICRA: Small RNAseq pipeline for paired-end reads.

Decription
Supplementary information
Documentation
License
Citation

Description

XICRA is a python pipeline developed in multiple separated modules that it is designed to take paired end fastq reads, trim adapters and low-quality base pairs positions, and merge reads (R1 & R2) that overlap. Using joined reads it describes all major RNA biotypes present in the samples including miRNA and isomiRs, tRNA fragments (tRFs) and piwi associated RNAs (piRNAs).

This pipeline resulted from the observation that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Paired end sequencing improves isomiR calling in small RNA sequencing data. Internal variation isomiR calls are frequent artifacts in single read sequencing data. Internal sequence variant isomiRs in single read sequencing mode may be false positives. See additional detail in the original publication here

So far, XICRA produces a miRNA or tRNA analysis at the isomiR or tRF level using joined reads or single-end reads, multiple software at the user selection and following a standardization procedure. Results are generated for each sample analyzed and summarized for all samples in a single expression matrix. This information can be processed at the miRNA or isomiR level (single sequence) but also summarizing for each isomiR variant type. This information can be easily accessed using the accompanied R package XICRA.stats. Although the pipeline is designed to take paired-end reads, it also accepts single-end reads.

See additional details on the code here. The workflow of the pipeline is described in the following image.

Installation

XICRA will require python v3.12 and java (we tested in openjdk 14 2020-03-17).

The XICRA python pipeline is available in pip and also available using conda.

XICRA depends on multiple third party software that we have listed here.

We encourage you to install XICRA and all dependencies using the conda environment we created and following these instructions.

Unfortunately, a couple of executables are not available neither as a conda or pip packages. These packages are miraligner and sRNAbench. We have generated a shell script to retrieve and include within your conda environment.

To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows:

1) Get requirements file from XICRA git repo

wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml

2) Create environment named XICRA and install required packages using conda:

conda env create -f environment.yml

3) Activate environment and install XICRA

## activate
conda activate XICRA

## install latest python code
pip install XICRA

4) Install missing software: Unfortunately, a couple of executables are not available neither as a conda or pip packages. These packages are miraligner, sRNAbench and MINTmap. We have generated a bash script to retrieve and include within your conda environment.

## install missing software
wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
sh installer.sh

To check everything is fine, try executing the config module:

XICRA config

To additionally check XICRA is working try to run a test example which is available within XICRA git repository

cd subset2test/
sh test_subset.sh

or available to download by executing the following command:

XICRA test
sh test_subset.sh

On the other hand, if you might have already installed software and available within your path, you might only need to install it using the XICRA pip module. We encourage you to installed it within a python environment. See as an example the description here

xicrastats

We additionally provide a supplementary R package for parsing and plotting some XICRA results. See additional details here.

Install it in R using:

# Install XICRA.stats version from GitHub:
# install.packages("devtools")
devtools::install_github("HCGB-IGTP/XICRA.stats")

Etymology

XICRA is the name in Catalan for a small cup of coffee or chocoate. Also, it was used as a small measure of milk, oil or wine (125 ml). See additional details here: https://ca.wikipedia.org/wiki/Xicra

Una xicra és tassa petita, més aviat alta i estreta, emprada expressament per a prendre la xocolata desfeta o cafè. També és una unitat de mesura de volum per a líquids que es feia servir a Catalunya per a l'oli, vi, o llet.

Supplementary Information

In this repository we provide supplementary information for the original paper describing the method. See additional details in folder BMC_bioinformatics_paper or here

Documentation

For a full documentation and details visit Read the Docs site here.

See a brief example on how to install and run XICRA here

License

MIT License

See additional details here

Developed and maintained by Jose F. Sanchez-Herrero and Lauro Sumoy at HCGB-IGTP

http://www.germanstrias.org/technology-services/genomica-bioinformatica/

Citation

Sanchez Herrero, J.F., Pluvinet, R., Luna de Haro, A. et al. Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. BMC Bioinformatics 22, 215 (2021). https://doi.org/10.1186/s12859-021-04128-1

HCGB-IGTP / XICRA

readme