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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 requires #39

Closed maocheng2020 closed 2 years ago

maocheng2020 commented 2 years ago

iRep requires high-quality draft genomes (>=75% complete, <=175 fragments/Mbp sequence, and <=2% contamination).But when I use checkm to calculate the assembly genome with a completeness of 60, I wonder why there are still results instead of NA? Should I first select an assembled genome that meets the requirements before calculating?There are too few assembled genomes that can fit <=2% contamination. Thanks!

christophertbrown commented 2 years ago

It is important to follow the guidelines for genome quality in order to be able to trust the results from iRep. We benchmarked these factors in the manuscript and found that going beyond the recommendations can result in skewed results.

Best,

Chris

On Apr 11, 2022, at 7:41 PM, maocheng2020 @.***> wrote:

 iRep requires high-quality draft genomes (>=75% complete, <=175 fragments/Mbp sequence, and <=2% contamination).But when I use checkm to calculate the assembly genome with a completeness of 60, I wonder why there are still results instead of NA? Should I first select an assembled genome that meets the requirements before calculating?There are too few assembled genomes that can fit <=2% contamination. Thanks!

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maocheng2020 commented 2 years ago

Thanks your for your reply. I'll filter out the draft genomes(<75% complete or >2% contamination) before run iRep.

maocheng2020 commented 2 years ago

@christophertbrown Hi. When I follow the guidelines of genome quality to calculate my data, I found that irep has values greater than 2. Your manuscript had described that "An iRep value of 1.25 would indicate that, on average, only one quarter of the cells are replicating" . My understanding is that irep values are in the range 1 to 2, right? How should I interpret values greater than 2? Thanks for the tools you developed.

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Anto007 commented 2 years ago

Not the developer of this tool but as a fellow user, my understanding is that iRep values > 2 are made possible by the occurrence of multiple replication forks at origin. Hope this info helps.

christophertbrown commented 2 years ago

Thanks for the response, Anto007! That is indeed exactly how I would explain this result.

Maocheng2020 - the data looks good to me. Although coverage is somewhat low the distribution and fit are clean.

Best,

Chris

On Jun 9, 2022, at 3:33 AM, Anto007 @.***> wrote:

Not the developer of this tool but as a fellow user, my understanding is that iRep values > 2 are made possible by the occurrence of multiple replication forks at origin. Hope this info helps.

— Reply to this email directly, view it on GitHub https://github.com/christophertbrown/iRep/issues/39#issuecomment-1150954496, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACS3G2KMOGTJ2J2HM476RS3VOHB6VANCNFSM5TFBRFZQ. You are receiving this because you were mentioned.