Why You Should Use alignment independent quantification for RNA-seq?

Alignment-independent tools are indistinguishable (only salmon shown) and more accurate than alignment-dependent workflows. gtf2table is more accurate than cufflinks for transcripts with >20\% unique sequence. Alignment-independent methods and gtf2table show higher accuracy with greater fraction unique sequence.

What is difference between alignment and mapping?

Find the approximate origin of a sequence. Alignment: Find the exact difference between two sequences.

What is the purpose of using two reads for alignment?

For example, short reads can sometimes align equally well to multiple locations (multi-mapped reads or multi-reads). Paired-end reads reduce the problem of multi-mapping, because a pair of reads must map within a certain distance of each other and in a certain order (Figure 8).

What is alignment mapping?

Alignment maps are organizational information radiators that help visualize the alignment of ongoing work with business outcomes. The work may be regular functionality addition or technical work such as re-architecting or repaying technical debt or improving the build and deployment pipeline.

What is area alignment?

The design principle of area alignment says that when you have a series of objects to be aligned that do not have regular shapes, that it is more aesthetically pleasing to centrally align them according to their area and weight than by central alignment of the bounding boxes.

What is RNA-Seq and next-gen sequencing?

The scope of Next-Gen Sequencing (NGS) and RNA sequencing (RNA-seq) are rapidly evolving and expanding. What is RNA-Seq? The central dogma of molecular biology has portrayed RNA as the intermediate molecule between DNA and protein, however this view is becoming increasingly outdated.

What is the theory behind RNA sequence alignment?

The theory behind aligning RNA sequence data is essentially the same as discussed earlier in the book, with one caveat: RNA sequences do not contain introns. Gene models in Eukaryotes contain introns which are often spliced out during transcription.

What are the Best Short read aligners for RNA sequencing?

One of the earliest and most popular is Tophat. Tophat is built on top of Bowtie ( another popular short read aligner aligned based on BWT ). (Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25:1105–1111.)

Do I need programming skills to analyze RNA-Seq data?

However, a general understanding of the principles underlying each step of RNA-seq data analysis allows investigators without a background in programming and bioinformatics to critically analyze their own datasets as well as published data.