Hi Qiime2 support team,
I am looking to merge together 3 different rep-seqs files from 3 different illumina runs so I can make a tree including all of these data. One of the runs was trimmed to 125 bp while the others are still 150 bp. Will I still be able to merge these rep-seqs files? I am seeing in the sequence files that the same sequence in the dataset trimmed by 25 bp gives a different feature id than the same sequence in the untrimmed dataset, so this makes me think that I will need to either trim my longer sequences or reprocess my trimmed sequences to be 150 bp.
Any advice on this topic?
Thank you so much for your time, I appreciate you Qiime2 support team!