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stschiff / msmc

Implementation of the multiple sequential markovian coalescent
GNU General Public License v3.0
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Questions of using MSMC decode on multiple haplotypes #19

Closed muhuaw closed 6 years ago

muhuaw commented 8 years ago

Hello Stephan,

Thank you for writing MSMC! It helps me to solve some important problems of my project. After using the default function of MSMC,

I am trying to use the decode function to estimate tMRCA states for my samples. However, when I use a file that contains four haplotypes as input for MSMC decode, it just output 40 columns instead of 240 columns as described in the manual. I used this file as input for two other functions of MSMC and it worked perfectly.

Here is a snapshot of my input file: chrXV 711 293 TCCC chrXV 1950 1063 TCCC chrXV 2333 215 AGGG chrXV 2410 31 CGCC chrXV 2448 38 TCTT chrXV 2838 267 TATT chrXV 2863 25 TGTT chrXV 3057 189 GAAA chrXV 3159 96 CCTT chrXV 3245 86 GAGG

Here is the command I used: local/msmc/build/decode -m 0.0015 -r 0.0012 PAXB07_LITC_UP_356_chrXV.msmc.txt > PAXB07_LITC_UP_356_chrXV.tMRCA.decode.txt

Do I need to specify in the command line there are four haplotypes in the input file? I read the help for decode function, it seems the script would automatically recognize how many haplotypes in the input. Thank you for your help.

Best Regards, Muhua

stschiff commented 8 years ago

Hi Muhua,

you are right, it seems I have implemented the decode script to output only the marginal state space, so the one that sums up the internal states per time interval. Indeed, the documentation says something different. Do you actually want to see all the states, though? It gets kind of complicated to plot and analyse… But it’s not a problem to implement that way in principle. Perhaps I’ll include a flag if all internal states are needed or so.

Stephan

P.S. Please post on the mailing list as well, CC’d.

On 5 Apr 2016, at 14:37, muhuaw notifications@github.com wrote:

Hello Stephan,

Thank you for writing MSMC! It helps me to solve some important problems of my project. After using the default function of MSMC,

I am trying to use the decode function to estimate tMRCA states for my samples. However, when I use a file that contains four haplotypes as input for MSMC decode, it just output 40 columns instead of 240 columns as described in the manual. I used this file as input for two other functions of MSMC and it worked perfectly.

Here is a snapshot of my input file: chrXV 711 293 TCCC chrXV 1950 1063 TCCC chrXV 2333 215 AGGG chrXV 2410 31 CGCC chrXV 2448 38 TCTT chrXV 2838 267 TATT chrXV 2863 25 TGTT chrXV 3057 189 GAAA chrXV 3159 96 CCTT chrXV 3245 86 GAGG

Here is the command I used: local/msmc/build/decode -m 0.0015 -r 0.0012 PAXB07_LITC_UP_356_chrXV.msmc.txt > PAXB07_LITC_UP_356_chrXV.tMRCA.decode.txt

Do I need to specify in the command line there are four haplotypes in the input file? I read the help for decode function, it seems the script would automatically recognize how many haplotypes in the input. Thank you for your help.

Best Regards, Muhua

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/stschiff/msmc/issues/19

muhuaw commented 8 years ago

Hi Stephan,

Thank you for the quick reply. I used MSMC to analyze separation of my populations. After getting the result for whole genome cross coalescence rate, I was wondering if I can get the cross coalescence rate for each genomic region. That’s why I was trying to use MSMC decode. I know this is not a proper way to do that. But I just want to know if I can get some useful result from genome scan.

Best Regards, Muhua

On Apr 6, 2016, at 10:38 PM, Stephan Schiffels notifications@github.com wrote:

Hi Muhua,

you are right, it seems I have implemented the decode script to output only the marginal state space, so the one that sums up the internal states per time interval. Indeed, the documentation says something different. Do you actually want to see all the states, though? It gets kind of complicated to plot and analyse… But it’s not a problem to implement that way in principle. Perhaps I’ll include a flag if all internal states are needed or so.

Stephan

P.S. Please post on the mailing list as well, CC’d.

On 5 Apr 2016, at 14:37, muhuaw notifications@github.com wrote:

Hello Stephan,

Thank you for writing MSMC! It helps me to solve some important problems of my project. After using the default function of MSMC,

I am trying to use the decode function to estimate tMRCA states for my samples. However, when I use a file that contains four haplotypes as input for MSMC decode, it just output 40 columns instead of 240 columns as described in the manual. I used this file as input for two other functions of MSMC and it worked perfectly.

Here is a snapshot of my input file: chrXV 711 293 TCCC chrXV 1950 1063 TCCC chrXV 2333 215 AGGG chrXV 2410 31 CGCC chrXV 2448 38 TCTT chrXV 2838 267 TATT chrXV 2863 25 TGTT chrXV 3057 189 GAAA chrXV 3159 96 CCTT chrXV 3245 86 GAGG

Here is the command I used: local/msmc/build/decode -m 0.0015 -r 0.0012 PAXB07_LITC_UP_356_chrXV.msmc.txt > PAXB07_LITC_UP_356_chrXV.tMRCA.decode.txt

Do I need to specify in the command line there are four haplotypes in the input file? I read the help for decode function, it seems the script would automatically recognize how many haplotypes in the input. Thank you for your help.

Best Regards, Muhua

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/stschiff/msmc/issues/19

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/stschiff/msmc/issues/19#issuecomment-206554104

stschiff commented 8 years ago

I see, OK, I leave this open as a feature request, and will let you know when it’s implemented.

Stephan

On 6 Apr 2016, at 22:49, muhuaw notifications@github.com wrote:

Hi Stephan,

Thank you for the quick reply. I used MSMC to analyze separation of my populations. After getting the result for whole genome cross coalescence rate, I was wondering if I can get the cross coalescence rate for each genomic region. That’s why I was trying to use MSMC decode. I know this is not a proper way to do that. But I just want to know if I can get some useful result from genome scan.

Best Regards, Muhua

On Apr 6, 2016, at 10:38 PM, Stephan Schiffels notifications@github.com wrote:

Hi Muhua,

you are right, it seems I have implemented the decode script to output only the marginal state space, so the one that sums up the internal states per time interval. Indeed, the documentation says something different. Do you actually want to see all the states, though? It gets kind of complicated to plot and analyse… But it’s not a problem to implement that way in principle. Perhaps I’ll include a flag if all internal states are needed or so.

Stephan

P.S. Please post on the mailing list as well, CC’d.

On 5 Apr 2016, at 14:37, muhuaw notifications@github.com wrote:

Hello Stephan,

Thank you for writing MSMC! It helps me to solve some important problems of my project. After using the default function of MSMC,

I am trying to use the decode function to estimate tMRCA states for my samples. However, when I use a file that contains four haplotypes as input for MSMC decode, it just output 40 columns instead of 240 columns as described in the manual. I used this file as input for two other functions of MSMC and it worked perfectly.

Here is a snapshot of my input file: chrXV 711 293 TCCC chrXV 1950 1063 TCCC chrXV 2333 215 AGGG chrXV 2410 31 CGCC chrXV 2448 38 TCTT chrXV 2838 267 TATT chrXV 2863 25 TGTT chrXV 3057 189 GAAA chrXV 3159 96 CCTT chrXV 3245 86 GAGG

Here is the command I used: local/msmc/build/decode -m 0.0015 -r 0.0012 PAXB07_LITC_UP_356_chrXV.msmc.txt > PAXB07_LITC_UP_356_chrXV.tMRCA.decode.txt

Do I need to specify in the command line there are four haplotypes in the input file? I read the help for decode function, it seems the script would automatically recognize how many haplotypes in the input. Thank you for your help.

Best Regards, Muhua

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/stschiff/msmc/issues/19

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/stschiff/msmc/issues/19#issuecomment-206554104

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/stschiff/msmc/issues/19#issuecomment-206560528

stschiff commented 6 years ago

Sorry, I have too many other points on my to-do list for MSMC and MSMC2 and will likely not implement this any time soon, so I'll close the issue.