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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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How to interpret results like "Segments=0+,12+,0-"? #6

Open kerenzhou062 opened 4 years ago

kerenzhou062 commented 4 years ago

Hi Jens,

How to interpret results like "Segments=0+,12+,0-"? There is only one segment in this cycle.

Best, Keren

jluebeck commented 4 years ago

Hi Keren,

This indicates a single segment, which is joined to the expected endpoints for the segment in the reference genome.

Jens

On Tue, Mar 24, 2020 at 6:51 PM Keren Chow notifications@github.com wrote:

Hi Jens,

How to interpret results like "Segments=0+,12+,0-"? There is only one segment in this cycle.

Best, Keren

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jluebeck/PrepareAA/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADM3Q4ZHYZONNY7KKZUK4CLRJFPRVANCNFSM4LTDUNAA .

kerenzhou062 commented 4 years ago

Hi Jens,

Thanks for your reply. What puzzles me is about the expected endpoints. Could you please explain more about it?

Best, Keren

jluebeck commented 4 years ago

If I understand the question correctly, in this case AA identified a segment of the genome (which was presumably amplified, though I cannot tell without seeing the estimated CN). The endpoints of the segment are determined by the segmentation analysis performed by AA. No discordant edges passing the AA filtering criteria were identified connecting the endpoints of the (presumably) amplified region to other, non-native locations in the genome.

kerenzhou062 commented 4 years ago

If I understand the question correctly, in this case AA identified a segment of the genome (which was presumably amplified, though I cannot tell without seeing the estimated CN). The endpoints of the segment are determined by the segmentation analysis performed by AA. No discordant edges passing the AA filtering criteria were identified connecting the endpoints of the (presumably) amplified region to other, non-native locations in the genome.

So according to your explanation, cases like this can be ignored when identifying ecDNAs?

Best, Keren

jluebeck commented 4 years ago

Correct, it does not have the discordant edges required to produce a cycle.

kerenzhou062 commented 4 years ago

Thank you so much, Jens!

Stay safe during this challenging time!

Best, Keren