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OTU picking with IMG #6

Open yi1873 opened 6 years ago

yi1873 commented 6 years ago

How to get OTU picking with IMG used metagenome sequencing data?

The shogun v0.0.1 couldn't installed by the commands you gave.

bhillmann commented 6 years ago

Can you send the commands you used to try and run your metagenomic sequencing data through BugBase?

I'm not sure if the current instructions are up to date anymore. The database for IMG has been foregone for RefSeq from NCBI. @TonyaWard Will know more.

yi1873 commented 6 years ago

Well, I just want to predict the Oxygen Utilizing of bacteria through BugBase used OTU.

But first, I need to get OTU picking result with IMG, so I tried to install shogun to use the command shogun_bugbase -i path_to_sequences -o output_path -u path_to_shogun_bugbase_db; but try pip install git+https://github.com/knights-lab/SHOGUN.git@v0.0.1 --no-cache-dir --upgrade failed.

To predict the Oxygen Utilizing of bacteria, do you have any suggestions?

Thanks !