Segmental duplications give false circle signals? about circle-map

[iprada]

Dear Chris,

Thanks a lot for the your suggestion.

This is usually a minor problem that keeps rolling around my head from time to time. As you have pointed out, the problem is caused by regions with homology, which cause that Circle-Map to output some erroneous calls. However, this erroneous identifications have always been a very small fraction of the datasets I have analyse, and the majority of the circles are always very well covered by sequencing ( Figure 2e in our preprint https://www.biorxiv.org/content/10.1101/654194v1.full). If this is not your case, let me know and I will think about what could I do.

As you have suggest, a good way to get around this would be to incorporate the coverage information in the final circle score. That is actually a great idea, and I will definitely consider to change the scoring model to one that takes into account the genomic read coverage within the coordinates.

Thanks a lot for the feedback!

Best regards,

Iñigo

[tchrisboles]

You're very welcome. I look forward to using Circle-Map again later this week (and to your future improvements). Best regards,

…

On Tue, Jul 30, 2019 at 8:30 AM iprada ***@***.***> wrote: Dear Chris, Thanks a lot for the your suggestion. This is usually a minor problem that keeps rolling around my head from time to time. As you have pointed out, the problem is caused by regions with homology, which cause that Circle-Map to output some erroneous calls. However, this erroneous identifications have always been a very small fraction of the datasets I have analyse, and the majority of the circles are always very well covered by sequencing ( Figure 2e in our preprint https://www.biorxiv.org/content/10.1101/654194v1.full). If this is not your case, let me know and I will think about what could I do. As you have suggest, a good way to get around this would be to incorporate the coverage information in the final circle score. That is actually a great idea, and I will definitely consider to change the scoring model to one that takes into account the genomic read coverage within the coordinates. Thanks a lot for the feedback! Best regards, Iñigo — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#22?email_source=notifications&email_token=AH7SXXNO6ZQCIPRGVG4EJN3QCAX7XA5CNFSM4IHTTEY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3DZYTY#issuecomment-516398159>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AH7SXXO5IVEFHCLJACSE6FLQCAX7XANCNFSM4IHTTEYQ> .