Merge feature tables of different length reads

Hi, hoping for some advice/insight into the best method for merging the feature tables of two sequencing runs. I’m aware that each run needs to be denoised individually before they can be merged. However, one of my runs in a 2x151bp and the other is a 2x251bp. Can they be merged with the different lengths or do I need to trim the 251 back to match? I can see pros/cons to both, but didn’t know if there was a common or best practice for dealing with this type of thing.

Thank you!
Alicia Reigel

Hi @reige012,
The trimming approach you mentioned would only work if the end product of both runs are of the exact same region and length. In this case your Forward primers should be the exact same and you trim all your reads to the same length. For example if you trim all your reads to 120 bp, will position 1 represent the exact same spot in both runs? If the answer is yes then merging them can work. If no, then you may consider some other method like fragment insertion that can deal with different region reads.

Thank you for this info.

One more question, should I merge the feature tables together and then run the taxonomy classification commands? Or should I run taxonomy on each feature table, remove anything that doesn’t classify and then merge the tables?

Thanks again!

Nevermind! I answered my own question. It seems I should merge them and then continue analyses if I’m reading the Fecal microbiota example correctly.

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