Farhan's blogs: An Optimistic View of a Bioinformatician

 Deseq is one of the most commonly used package to calculate differential gene expression using R. In the following video, we using windows OS and R software to perform different expression analysis using DESEQ2 package. However, the same method can be performed on any of the following platforms:  Mac Windows Linux The following video will guide you through the steps of Deseq analysis.

 The final step is to calculate the gene expression values from the sorted indexed BAM file.  There are different ways to calculate the gene expression. However, here we will show FeatureCounts method to calculate the gene expression counts. The following video will guide you through the steps:  

 This is the second last step of processing RNA-seq files. Here we will show how the BAM files are indexed. The following video will guide you through the steps:  

 The following video will guide you through the step of converting Fastq to BAM file:

The poor quality reads and potential adapter sequences present in your file can be removed using the trimmomatic algorithm. The following video will guide you through the process of how to remove the poor quality reads from your fastq file. #Adapater #Sequences #Linux #Ubuntu

 After generating the Fastq file, first thing you need to check is the quality. The following video will guide you through the process that how to check the quality of fastq files using FASTQC Algorithm. #Fastqc