Quantifying repetitive elements in RNA-seqs
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4.1 years ago
lkianmehr ▴ 70

Hello,

Could you please give an almost easy quantification method suggestion for repetitive elements in RNA-seq data and how can I see repetitive elements sequences for comparing between two RNA-seq reads?

thanks in advance

RNA-Seq repetitive elements quantification • 1.6k views
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4.1 years ago
Martombo ★ 3.0k

If you're quantifying genetic elements that are present in multiple copies in the genome, with little variation, you can use a rather standard approach: collect representative sequences you want to study and map and count your reads against that (allowing for a higher number of mismatches than usual). An example of this would be snRNAs, that can have 10s to 100s of copies in the genome and a few nucleotide changes each.

If you're after actual repetitive / transposable elements, there are programs designed for their quantification: check out TEToolkit. Programs like TEToolkit can also give you information about families of TE.

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