I understand that I can filter the tables using "qiime taxa filter", but I was wondering if there was a way to filter the results to include the top 50-100 hits based on the metadata file/column provided.
What do you mean by "top 50-100 hits"? Do you mean the 100 most abundant taxa or something along those lines?
See qiime feature-table filter-features. This will allow you to filter features either based on abundance or based on a list of features you want to select or exclude, or based on some feature metadata.
Specifically for the heat map, I want to "zoom in" on the top features to see what might be causing them to be different.
Honestly, I need to cut down the number of reads, but I don't really know how to do it. Just running the top 100 taxa probably would help a lot. I will try to figure out how to do that.
Another thing, I thought might be a good idea was to combine reads that are all from the same metadata category. Is this something I can do? And is it advised?
Thank you again for your help. I apologize for my lack of description and comprehension.
Use qiime feature-table filter-features, setting the min frequency at an appropriate level.
Do you mean group samples that share the same sample metadata value? See qiime feature-table group. Definitely not a bad idea when making heatmaps if you have many groups...
