Filtering reads by ID sample and taxa

Hi everyone,

I’m trying extract representative reads for Lactobacillus sp. using qiime taxa filter-seqs but I do not have ID sample information in output table. How could I get reads for Lactobacillus sp and ID sample information in output file?

Hi @Gislaine_Curty,
See the qiime taxa filter-table method — that will filter a feature table (sample X observation matrix). The method you are using only filters out the sequence file.

Good luck!

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Hi @Nicholas_Bokulich, thank you for your answer.

Then, I need to get Lactobacillus read sequences per ID_sample for I do sequence analysis in the samples. I guess that in qiime taxa filter-table I will just have the reads count.

That will have the read count per sequence ID, and the sequence file will tell you what the sequences are for each of those IDs.

These sequences most likely overlap in many of your samples, so extracting sequences per sample would be cumbersome, but possible (e.g., use filter-seqs to filter out lactobacillus, then use qiime feature-table filter-samples to filter out seqs belonging to each individual sample).

What are you trying to accomplish? Maybe I can suggest a better way, or maybe I am misunderstanding your goals with my answer.

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