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Post Alignment Reads Quantification of the Pig Transcriptome Sequencing
Next generation sequencing - RNA-seq technology is a powerful tool which creates new possibilities in whole transcriptome analysis. The proper reads quantification, is an essential element of receiving the relevant analysis results. The aim of the present work was to illustrate the post alignment reads quantification as an important element in RNA-seq pipeline. As an example, we considered 22 samples selected from 4 pig breeds (Polish Landrace, Polish Large White, Pietrain and Pulawska) to analyse global changes in transcriptome form the muscle tissue. Bowtie2 output alignments for each sample were subjected to RNA-SeQC quality control before continuing with differential expression analysis. Considering changes between the mean coefficient of variation and the mean per-base coverage for genes with low, middle and high expression, two samples were excluded from the further analysis.
Keywords:
reads quantification
post-alignment
RNA-Seq
pig
