BAQCOM

BAQCOM - Bioinformatics Analysis for Quality Control and Mapping <br>

Quality Control (Trimmomatic), Mapping (STAR | HISAT2) and Counting Reads (HTSeq | featuresCount)

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BAQCOM is an user-friendly pipeline which implements five automated pipelines for RNA-Seq analysis using Trimmomatic for QC, STAR or HISAT2 for mapping and, HTSeq or featuresCount for counting reads. <br> <br> <br>

<a href="https://ibb.co/tsTGtSf"><img src="https://i.ibb.co/gTL2pG1/baqcom-steps-white.png" alt="baqcom-steps-white" border="0" width="900"></a>

STEP.1 - Download this repository to a preference path:<br>

Git is required

 git clone https://github.com/hanielcedraz/BAQCOM.git
 cd BAQCOM
 chmod +x install.sh
 ./install.sh

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STEP.2 - Install R<br>

To install R Access <a href="https://cran.r-project.org">CRAN website </a> <br> <br>

STEP.3 - Install MultiQC and HTSeq-count:

MultiQC: If you would like to use multiqc analysis, please install it.<br> Installation: If pip is not installed, please install as follow:

	wget https://bootstrap.pypa.io/get-pip.py -O get-pip.py
	python get-pip.py

You can install MultiQC from PyPI using pip as follow:

	pip install multiqc

More information, please access <a href="https://github.com/ewels/MultiQC"> MultiQC website</a>

HTSeq-count: <br>

HTSeq is available from the Python Package Index (PyPI):
	To use HTSeq, you need Python 2.7 or 3.4 or above (3.0-3.3 are not supported), together with:
		NumPy, a commonly used Python package for numerical calculations
		Pysam, a Python interface to samtools. 
	To make plots you will need matplotlib, a plotting library. 

You can install HTSeq-count using pip:

	pip install HTSeq
	
If HTSeq is already installed you need to upgrade it
	pip install HTSeq --upgrade

In addition you need to upgrade numpy
	pip install numpy --upgrade

<a href="https://htseq.readthedocs.io/en/release_0.11.1/install.html">or following the source documentation</a>

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STEP.4 - Install PigZ:

To speed up your analysis results, install the pigz.

Centos

sudo yum install pigz

Ubuntu

sudo apt install pigz

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Examples

You can find some command line examples <a href="https://github.com/hanielcedraz/BAQCOM/blob/master/examples/examples.md">here</a> <br> <br> <br>

Differential Expression Gene

You will find some script to analyze differential expression genes <a href="https://github.com/hanielcedraz/DiffExpressGenes.git">here</a>

<a href="https://github.com/hanielcedraz/BAQCOM/blob/master/RELEASE_notes.md">RELEASEnotes</a>