Question: How chimeras reads generated in PacBio?
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gravatar for Medhat
4.3 years ago by
Medhat8.8k
Texas
Medhat8.8k wrote:

As it is declared in my question, I would like to know if anyone have an idea how chimera formed in SMRT PacBio sequencing?

here Thomas Hackl try to explain it; but I would like to have more explanation. also what is siamaeras?

sequencing • 2.1k views
ADD COMMENTlink modified 4.2 years ago by rhall160 • written 4.3 years ago by Medhat8.8k
3
gravatar for rhall
4.2 years ago by
rhall160
United States
rhall160 wrote:

SMRT Bells are blunt end ligated to the DNA fragment being sequenced, even if they are in an excess there is a non-zero chance of a DNA fragment ligating to another DNA fragment before having a SMRT Bell adapter added. This would generate the classic chimera, a sequenced read being from two random parts of a genome. Note this is random and will not happen at exactly the same location more than once, so it is easily dealt with at the analysis stage. The "siamaeras" or missing adapter look like a sequence followed by the reverse complement of the sequence, and results from the SMRT Bell being missing / not-detected on one end of the insert i.e. you read a sequence forward then backwards without an adapter so the software does not know that the read needs to be split. This can happen due to sample prep - a long overhang forms a hairpin, mimicking a SMRT Bell, or less frequently due to a real SMRT bell being missed in software. See the template prep guide for more info

ADD COMMENTlink written 4.2 years ago by rhall160
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