Closed maocheng2020 closed 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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Thanks your for your reply. I'll filter out the draft genomes(<75% complete or >2% contamination) before run iRep.
@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.
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.
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.
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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!