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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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What happens if you use a smaller Seed? #64

Open newpest opened 4 weeks ago

newpest commented 4 weeks ago

If I manually split a 300kb seed into two 100kb seeds, what is the difference in the AA running results?

jluebeck commented 4 weeks ago

Answer really depends on what the seed represents. In many cases, those two seeds will become joined again into one AA amplicon because they share continuously high CN and probably SVs that link them. Feel free to try it out and see for yourself. :)

If you're splitting seeds because of long runtimes, you can also consider trying to set --AA_insert_sdevs 9.

newpest commented 4 weeks ago

The seeds generated by CNV detection by Cnvkit seem to have higher resolution than the seeds obtained by readDepth Seeds by ReadDepth:

8       130540901       131268201       5.796678958040257
8       132769401       133678001       7.199149293492551

Seeds by cnvkit:

8       130336500       133681505       6.785932467648188

Amplicon detected by ReadDepth Seeds has a long low-copy fragment compared to Cnvkit, which ultimately affects the classification results of AC.

jluebeck commented 4 weeks ago

Interesting, thanks - if this is a public sample which you can point me to I'm happy to dig in further.