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Old 11-26-2015, 09:22 AM   #1
roliwilhelm
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Location: Ithaca, NY

Join Date: Jun 2012
Posts: 38
Default How To Run 'Merge' in the Wonderful New checkM Package

I have produced a number of draft genome bins from a series of metagenomes. Using checkM, I have run the typical workflow ("checkm lineage_wf") and produced a number of helpful outputs. However, I would now like to run the "merge" command to see if any of my recovered draft bins might be merged. It requires a 'Marker Set' (aka 'Marker File') of which I know nothing. I tried feeding it the 'lineage.ms' (assuming the .ms stands for 'marker set') which was generated by the generic workflow, but received the following error: " Merge command requires a taxonomic-specific marker set or a user-defined HMM file."

Could you please suggest what file to use, or how to generate a marker set?

Thanks in advance!
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