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

[kerenzhou062]

Hi Jens,

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

Best,
Keren

[jluebeck]

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

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On Tue, Mar 24, 2020 at 6:51 PM Keren Chow ***@***.***> 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 <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADM3Q4ZHYZONNY7KKZUK4CLRJFPRVANCNFSM4LTDUNAA> .

[kerenzhou062]

Hi Jens,

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

Best,
Keren

[jluebeck]

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]

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]

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

[kerenzhou062]

Thank you so much, Jens!

Stay safe during this challenging time!

Best,
Keren