Unexpected sequence trimming in feature-table merge-seqs


I am trying to combine two databases to get a more detailed assignment for my species of interest later on.

I use the complete RDP database and a subset of greengenes database features. Everthing works fine until the actual merging step. The command is:

Qiime feature-table merge-seqs
–i-data greengene_filter.qza
–i-data rdp_seq.qza
–o-merged-data rdp_green_seq.qza

The resultung merged output file contains all greengenes sequences but all rdp sequences are trimmed to a certain sequence length. Funnily they are all trimmed right behind my primer sequence but I didn’t mention the primer sequence anywhere in my commands so far… I am using generel 16S primer which are present in every sequence. For me, it looks like the merging command alignes the rdp OTUs to the greengenes ones and trimmes them right behind the aligned part which ends up being exactly my primer sequences as they occur in every sequence.

How can I merge them without loosing any sequences? Am I missing any default settings?

Many thanks in advance for your help!

Hi @Barbs!

Can you go back and double-check that the sequences in rdp_seq.qza aren’t already trimmed? This command doesn’t do any trimming (in fact, it is just a general-purpose table merge - these data could be anything, credit card numbers, favorite pokemon, baby names, etc - the point is that the fact that it is sequences is almost incidental).

If that doesn’t clarify things, can you please provide us with download links to your artifacts (inputs and outputs)? Then we can take a closer look and get to the bottom of this. Thanks! :t_rex:

Hi @thermokarst,

you were right! One of my artifacts was a trimmed version from a previous analysis. I double checked them before I posted this but apparently I missed one artifact. So sorry for wasting your time! Next time I check everything once more!

Thanks a lot!

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Hi @Barbs! That is great news! No apology necessary - and I certainly don’t think that is a waste of time. I make those kind of mistakes all the time, I totally get it! Happy QIIMEing! :sun_with_face:

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