What is RNA-seq alignment?

Alignment is the algorithm to figure out which gene a read came from. Basepair provides the popular STAR and TopHat tools [2,3]. Another option if your species has no reference is to assemble your own transcriptome using Trinity, which is also offered on Basepair [4].

Which bioinformatics software can you use for pathway analysis for the set of differentially expressed genes obtained from your RNA sequencing analysis?

GPSeq This is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.

Why do Bioinformaticians often prefer to display fold change as a Log2 value?

Log2 aids in calculating fold change, by which measure the up-regulated vs down-regulated genes between samples. Usually, Log2 measured data more close to the biologically-detectable changes.

What is the purpose of RNA-Seq analysis?

RNA-seq (RNA-sequencing) is a technique that can examine the quantity and sequences of RNA in a sample using next-generation sequencing (NGS). It analyzes the transcriptome, indicating which of the genes encoded in our DNA are turned on or off and to what extent.

What is deg in bioinformatics?

Comprehensive service typically 4-8 weeks: QC of data, alignment to reference and list of differentially expressed genes (DEG) using pre-defined statistical/filtering thresholds. Gene function analysis and systems biology: e.g. gene ontology, pathway and network mapping. …

What is contig in bioinformatics?

A contig–from the word “contiguous”–is a series of overlapping DNA sequences used to make a physical map that reconstructs the original DNA sequence of a chromosome or a region of a chromosome. A contig can also refer to one of the DNA sequences used in making such a map.

What is the difference between fold change and log2 fold change?

Fold change is calculated simply as the ratio of the difference between final value and the initial value over the original value. To make this leveled, we use log2 for expressing the fold change. I.e, log2 of 2 is 1 and log2 of 0.5 is -1.

What does a negative log2 fold change mean?

If we use log2(fold change), fold changes lower than 1 (when B > A) become negative, while those greater than 1 (A > B) become positive. Now the values are symmetrical and it’s easier to see fold changes in both directions on one plot.

What is the main challenge with RNA-Seq alignment to a reference genome?

The major challenge in RNA-Seq data analysis is the accurate mapping of junction reads to their genomic origins. To detect splicing sites in short reads, many RNA-Seq aligners use reference transcriptome to inform placement of junction reads.

Is RNA-Seq quantitative?

This approach, called “RNA-seq”, can generate quantitative expression scores that are comparable to microarrays, with the added benefit that the entire transcriptome is surveyed without the requirement of a priori knowledge of transcribed regions.