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christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
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iRep and bPTR values lower than one #32

Closed yilmazbah closed 4 years ago

yilmazbah commented 4 years ago

Dear all, When we analyzed our dataset using your pipeline, we got values lower than 1 for samples in bPTR analysis. Can you explain me what is the meaning of having values lower than one both for iRep and bPTR? Any thought will be useful. Thank you so much. Best wishes, Bahti

christophertbrown commented 4 years ago

Hi Bahti,

Values lower than one are an artifact of the PTR method. This happens when coverage at the origin and terminus are very similar, and random variation in coverage causes the terminus to be higher than at the origin. It also indicates that there may have been an issue correctly identifying the location of the origin and/or terminus of replication.

iRep is calculated differently, and as such it is not possible to have values lower than one. Values of one, or close to it, indicate a lack of replication.

Hope this helps!

Chris

On Oct 23, 2019, at 5:56 AM, Bahtiyar YILMAZ notifications@github.com wrote:

 Dear all, When we analyzed my data using your pipeline, we got values lower than 1 for samples in bPTR analysis. Can you explain me what is the meaning of having values lower than one both for iRep and bPTR? Any thought will be useful. Thank you so much. Best wishes, Bahti

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yilmazbah commented 4 years ago

Hey Chris,

Thank you so much for your help and explanation. This is really helpful. I think those samples of mine should be lack of replication.

Thanks a lot for your time.

All the best, Bahti