Jose Manuel Martí

Hi! I think it would be very nice to have those preferences (or any other) also available through the Krona XML specification. Maybe I can help with that part. I...

@ondovb, @lskatz, all right, so I understand that the XML spec should be changed as a prerequisite for including those options in the command line, is that right? In that...

Hi @rjsorr and thanks for reporting about this. The behavior that you are seeing when you only use one negative control and one regular sample is normal, since the "EXCLUSIVE"...

Thanks, @rjsorr, for the feedback. After thinking on different options, I found that one of the already existing options for Recentrifuge's main script was the best choice. It's the `--summary`...

Thanks @rjsorr. Did you get 360 MB even with the `--summary ONLY` option? How many samples does that dataset have? I guess I will have to consider splitting the html...

OK, thanks, @rjsorr. Datasets are now very easily reaching hundreds of samples. Are you using the last release of recentrifuge? The option `-u only` should throw an error now, with...

Hi @rjsorr, sorry, I don't understand it well... do you mean "abundance tables" after the contamination removal? Any column in the output where you see `_CTRL_` in the name is...

Hi @arz19893, About your first question, in general, most of the organisms present in the negative controls are removed from the regular samples, but the final outcome depends on your...

Hello @lvelosuarez! Many thanks for the introduction! I appreciate that you take some time/words to let me know about your work and your use case for Recentrifuge. :) That's a...

Hi @rjsorr, For any downstream processing, you don't want to use the HTML output but Recentrifuge's "extra" output or the pickled (serialized (output). These are the relevant options for you:...