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Changes between Version 3 and Version 4 of SOPs/rna-seq-diff-expressions_TE

v3	v4
3	3	=== Background ===
4	4
5		* Transposable elements make up between 20 to 80% of the genome sequence for many eukaryotes, yet are typically excluded from the analysis that follows transcriptomic profiling with RNA-seq. This exclusion is due to the repetitive nature of transposons and the ambiguity that accompanies assigning multi-mapping reads.
	5	* Repetitive elements comprise a substantial portion of many eukaryotic genomes. In humans, for example, estimates of the repetitive fraction of the genome range from [https://www.pnas.org/content/111/17/6131.full 1/2] to more than [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228813/ 2/3]. Moreover, repetitive elements are known to play an important role in cellular function and disease, yet are typically excluded from the analysis of high-throughput sequencing experiments. This exclusion is due to the ambiguity that accompanies assigning multi-mapping reads.
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7	7	=== Step by step analysis ===