3  Package Installation

3.1 Install FastQC

  • The first step of RNA_Seq data analysis is to check the quality of the sequencing data in .fastq/.fq file format.

  • FastQC is the commonly used tool to perform quality control.

conda install -c bioconda fastqc
  • To check whether installation is complete or not, just type in the terminal the following.
fastqc -h

3.2 Install Trim galore

  • Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control.

  • If adapter content is found then adapter should be removed using Trim Galore.

conda install -c bioconda trim-galore
  • To check the successful installation
trim_galore -help

3.3 Install STAR aligner

  • The alignment process involves performing the read alignment using one of several splice-aware alignment tools such as STAR or HISAT2.

  • The choice of aligner is often a personal preference and also dependent on the computational resources.

conda install -c bioconda star

STAR -h

3.4 Install subread

  • Once alignment is complete, the next step would be to count of aligned reads to each gene.

  • featureCounts is a part of the subread toolkit which is used for this purpose.

conda install -c bioconda subread

featureCounts -h
Note

Initial QC to be done using FastQC, followed by trimming with TrimGalore!. Reads will be aligned using STAR and overlaps to be counted with featureCounts.

3.5 Install MultiQC

  • MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.
conda install -c bioconda multiqc

multiqc -h