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Old 04-28-2016, 10:47 AM   #1
nucleus
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Location: Albany,ny

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Default Hi-C Metagenomics

Does anybody has experience with metagenomics clustering using Hi-C data? We generated data using Hi-C on a bacterial mixture and were planning to do the binning/clustering with MetaPhase (github.com/shendurelab/MetaPhase). Unfortunately, this repository is apparently broken beyond repair and we are left with no easy way to analyze this data. If someone knows an alternative that we could use,we will be very grateful to hear about it.

Thanks.
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Old 05-13-2016, 11:47 AM   #2
RaqMan
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Hi, I am also new in the Hi-C and I just downloaded MethaPhase from the repository with no problem (with the test files it looks like is working). Does it breaks when you use it with your Hi-C data? If it does what kind of error do you have? This could help me in potential future problems.

Thank you in advance!
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Old 05-13-2016, 12:08 PM   #3
nucleus
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This is strange. I cant get it to compile because of missing modules. For example, LinkMatrix is looking for TimeMem.h which is absent from the repository. I know of other modules that are missing as well.

This is the error I get with 'make':

g++ -c TextFileParsers.cc -Wall -g -O3 -ansi -pedantic -I/home/pxl10/include -I/net/shendure/vol10/jnburton/extern/samtools-0.1.16
g++ -c LinkMatrix.cc -Wall -g -O3 -ansi -pedantic -I/home/pxl10/include -I/net/shendure/vol10/jnburton/extern/samtools-0.1.16
LinkMatrix.cc:13:21: fatal error: TimeMem.h: No such file or directory
compilation terminated.
make: *** [LinkMatrix.o] Error 1
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Old 05-14-2016, 12:43 PM   #4
RaqMan
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Did you use github to clone the complete repository in your computer? I got the repository from the same link that you posted and I have that file in the src folder.

What I would do is to download it again and see if that works. (I checked and at list TimeMem.h is there).

Hope that helps.
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