Merging feature-tables with different samples

[Unai_Ortega]

Hello, I am new in bioinformatics and I don´t have much idea in working with bacteria DNA data. I made 2 runs of Iluminaseq of different soil samples and i recieved all the results with the feature analysis done. Now i want to merge all the samples but i don´t know how to proceed. I obtained for the two runs a denoising_table.qza with the frecuencies of the ASVs which IDs are indentified like this (6e7604ec6f61c2fee0d97a8d8b3d057d...), a feature_table.qza in which features are identified like this (ASV1,ASV2...), a feature_sequence.qza that has a fasta document that especifies the secuence of each ASV identified in the same way as the feature_table and finally the taxonomy asigned to each ASV.

If I use the denoising tables to merge de runs i obtain the result that i want buecause the IDs of both tables refer to the same secuences but I dont know how to merge the secuences as they are identified with other labels (ASV1,ASV2...). If anyone can tell me how I should proceed I would appreciate it.

[buzic (Victoria)]

Hi @Unai_Ortega ,

Welcome to the Forum.

From what I understand you have sequencing runs that were processed up to the point of denoising and now you have an abundance table and sequence table from two runs, and you'd like to merge them for downstream analysis?

If they have been denoised with the same parameters, the ID's will match up as they are generated from the sequences.

If I've got that correct you can merge them like so for the abundance tables :

qiime feature-table merge \
--i-tables A_table.qza \
--i-tables B_table.qza \
--o-merged-table merged-table.qza

For the sequence files:

qiime feature-table merge-seqs \
--i-data A_rep-seqs.qza \
--i-data B_rep-seqs.qza \
--o-merged-data merged-rep-seqs.qza

Hope that helps, there is a good tutorial here if you'd like some more tips.