16S OTU tables: merging tables and loosing information

Question

[chiara.conte91]

Hello there, I run 16S RNA analyses with Qiime. I am facing an issue in the final step. I run the analyses of two distinct batches of samples and then I merged the OTUs tables. I found out a huge loss of information in terms of the number of OTUs and the number of sequences per sample compared to the OTU table from each distinct run. I tried then to merge the sequences (cat seqs.fna, seqs.fna> merged.fna) and the mapping files after demultiplexing and run the whole downstream analyses. I gained the same results of merging the OTU tables at the end of the two individual runs.

Does anybody know what is due to this loss of information and how to avoid this?

thanks, everybody for your kind attention and help!

Answer 1

[Erwann]

Hello Chiara,

How did you exactly use the feature-table merge command ?

It makes sense to have "less" OTUs after merging, as some OTUs may be shared by the two tables. You should have as many OTUs as the union of OTUs from run 1 and OTUs from run 2. However, as far as I know, it should not impact the number of reads per sample. Erwann