Abnormal results of MSMC, and need help ~ about msmc

[stschiff]

Hi, artefacts at the boundaries of the curves can happen. Overall the results look pretty clean to me, though, you get a good midpoint estimate for all curves, right? Have you tried msmc2 already? It might get you cleaner results (www.github.com/stschiff/msmc2 <http://www.github.com/stschiff/msmc2>). Best, Stephan

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On 8 Apr 2019, at 07:05, Yun-HongWu ***@***.***> wrote: In my MSMC analysis, The genome data sets of one individal (means two phased haplotype genomes) from each population was picked out, and i did the relative CCR analysis (population split) between each population pair. But in my results i found, for some population/species pairs, the RCCR value can't be zreo even at very recent time point. Is my results normal? and what does this pattern mean? <https://user-images.githubusercontent.com/48516488/55699733-cef15b00-59fe-11e9-875c-8d85aaeb32bc.png> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#43>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAbQmj0lZJDYCs79jbLNQE5ou9kK0QnYks5ves4cgaJpZM4chTgq>.

[Yun-HongWu]

Hi, artefacts at the boundaries of the curves can happen. Overall the results look pretty clean to me, though, you get a good midpoint estimate for all curves, right? Have you tried msmc2 already? It might get you cleaner results (www.github.com/stschiff/msmc2 http://www.github.com/stschiff/msmc2). Best, Stephan
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On 8 Apr 2019, at 07:05, Yun-HongWu @.***> wrote: In my MSMC analysis, The genome data sets of one individal (means two phased haplotype genomes) from each population was picked out, and i did the relative CCR analysis (population split) between each population pair. But in my results i found, for some population/species pairs, the RCCR value can't be zreo even at very recent time point. Is my results normal? and what does this pattern mean? https://user-images.githubusercontent.com/48516488/55699733-cef15b00-59fe-11e9-875c-8d85aaeb32bc.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#43>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAbQmj0lZJDYCs79jbLNQE5ou9kK0QnYks5ves4cgaJpZM4chTgq.
Dear Stephan, thanks for your reply~ Next i will try MSMC2. But i have a few questions i'd like to discuss with you.
First, i just used the mask files of high-depth bams (generated by your tool bamcaller.py) and the vcf files (not from bamcaller.py tool ,it's generated from GATK protocol and phased by SHAPEIT2 with population data sets) to get the final msmc input files. So is my process reliable ?
Second in my data sets, these samples are from five closely related species (the divergent time of TMRCA is about 1.4~2.0 Mya), but i found the estimated divergent time of MSMC for each species pair is very recent (the most divergent time is just about 300 Kya), so does it mean the msmc does not fit my data sets?
Third, actually i did not estimate the midpoint for all curves, i just marked the 0.5 RCCR position with R 'abline' function and could you tell me how to get this midpoint estimate?

Best,
Hong