Are the coordinates in *_cycles.txt in 1-based format?

[kerenzhou062]

Hi Jens,

As in the title, are the coordinates in *_cycles.txt in 1-based format?

Best, Keren

[jluebeck]

Hi Keren,

Both graph and cycles files are 0-based. (Edited to correct answer)

On Mon, Feb 24, 2020, 12:35 PM Keren Chow notifications@github.com wrote:

Hi Jens,

As in the title, are the coordinates in *_cycles.txt in 1-based format?

Best, Keren

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[kerenzhou062]

Thank you so much, Jens!

[Si-Nan]

Hi Jens, The explanation about coordinate in AA readme is 0-based in graph file section.

{POS}: 0-based coordinate where the basepair of said coordinate is included in participating segment. If the actual position is unknown or outside the amplicon interval, then {POS} is set to -1 corresponding to the source vertex.

By the way, I have read your explanation in readme of AA and this issue about +/- sign. But I'm still confused about it. Could you please explain this more clearly with diagrams?

+/- indicates that the participating segment ends on the right or begins on the left of the corresponding basepair respectively

SequenceEdge section in graph file sequence chr7:54729879- chr7:54830971+ 3.091732843468521 10.2908940993 101092 10954

BreakpointEdge section in graph file concordant chr7:54830971+->chr7:54830972- 3.0917328434685207 9 None None

I'm not sure the meaning of +/- in these parts.

Thanks !

Best, Sinan

[Si-Nan]

I draw a diagram to show coordinate in graph file. Do you think I did the right thing?

[jluebeck]

Hi,

Thank you for pointing out the error in the previous reply - the AA Readme is correct - they are 0 based.

The diagram you drew for the graph file is entirely correct. And to clear up any confusion, yes, the +/- for the elements of the cycles file is different than the +/- of the elements in the breakpoint graph file.

Thanks and best regards, Jens

[kerenzhou062]

Hi,

Thank you for pointing out the error in the previous reply - the AA Readme is correct - they are 0 based.

The diagram you drew for the graph file is entirely correct. And to clear up any confusion, yes, the +/- for the elements of the cycles file is different than the +/- of the elements in the breakpoint graph file.

Thanks and best regards, Jens

Hi Jens,

I also checked the AA README before asking you about the format about coordinates in *_cycles.txt file.

I ran AA on my WGS data and found that the start and end positions of Segment-52 in amplicon216 were exactly the same (please check the attached file).

Could you please explain more about this result?

Best, Keren

XXX_amplicon216_cycles.txt

[jluebeck]

Hi Keren,

If this happens, it is usually because the same coordinate is used as a breakpoint going to more than one discordant location. If such a segment appears in a decomposition, you can ignore it. For Cycle29 in your attached file, which uses segment-52, instead of 20+,52+, you can assume the decomposition is instead just '20+'.

Best, Jens

On Mon, Dec 14, 2020 at 5:12 PM Keren Chow notifications@github.com wrote:

Hi,

Thank you for pointing out the error in the previous reply - the AA Readme is correct - they are 0 based.

The diagram you drew for the graph file is entirely correct. And to clear up any confusion, yes, the +/- for the elements of the cycles file is different than the +/- of the elements in the breakpoint graph file.

Thanks and best regards, Jens

Hi Jens,

I also checked the AA README before asking you about the format about coordinates in *_cycles.txt file.

I ran AA on my WGS data and found that the start and end position of segment-52 in amplicon216 are exactly the same (please check the attached file).

Could you please explain more about this result?

Best, Keren

XXX_amplicon216_cycles.txt https://github.com/jluebeck/PrepareAA/files/5692526/XXX_amplicon216_cycles.txt

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[kerenzhou062]

Hi Keren, If this happens, it is usually because the same coordinate is used as a breakpoint going to more than one discordant location. If such a segment appears in a decomposition, you can ignore it. For Cycle29 in your attached file, which uses segment-52, instead of 20+,52+, you can assume the decomposition is instead just '20+'. Best, Jens … On Mon, Dec 14, 2020 at 5:12 PM Keren Chow @.**> wrote: Hi, Thank you for pointing out the error in the previous reply - the AA Readme is correct - they are 0 based. The diagram you drew for the graph file is entirely correct. And to clear up any confusion, yes, the +/- for the elements of the cycles file is different than the +/- of the elements in the breakpoint graph file. Thanks and best regards, Jens Hi Jens, I also checked the AA README before asking you about the format about coordinates in _cycles.txt file. I ran AA on my WGS data and found that the start and end position of segment-52 in amplicon216 are exactly the same (please check the attached file). Could you please explain more about this result? Best, Keren XXX_amplicon216_cycles.txt https://github.com/jluebeck/PrepareAA/files/5692526/XXX_amplicon216_cycles.txt — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADM3Q4ZIJMIL64NFSFXDKX3SU2ZZJANCNFSM4K2M3C7A .

Hi Jens,

Thank you for your information.

Best, Keren