Questions tagged [mappability]

When speaking of a sequencing read and a reference genome, the ability of an algorithm to determine the origin of the read in the genome. If the read can be unequivocally located in the reference genome, it has high mappability. If the read can be mapped to multiple loci, it has intermediate mappability. If the read cannot be mapped to any locus, it has low or no mappability.

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Why total RNA-seq usually yields low mapping rate?

Maybe this is a silly question, but I'm really wondering why we usually get low mapping rates if we map total RNA-seq, but not poly(A)-enriched (in particular, for human, mouse, and zebrafish datasets)...
6
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1answer
104 views

Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?

I believe that the human genome reference took DNA samples from different people and that some natural variation is included in extra contigs. However, the human reference genome comes from a ...
5
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2answers
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GRCh38 centromeres mappability

Is the mappability of the centromeres in the GRCh38 genome reference similar to each other? As far as I can remember when GRCh38 came out, the sequence of the centromeres was determined by a ...
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2answers
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Mapping Reads to Known Gene Paralogs with Long Read Technology

I have some sequencing data from a captured region that is a known paralog edited. For now, I have been mapping the data using standard minimap2 flags for PacBio DNA sequencing: ...