Paired end reads too short for merging. Gap aware merging possible?


I have a ~500 bp sequence, and I sequenced it by using a 2x150 bp kit (result of communication error). Therefore, there's like a 200 bp gap that is in the middle of the read that isn't being sequenced. Is there a way to tell Qiime to expect a gap of around 200 bp, so that the OTU assignment will be based on the flanking 150 bp regions? Is this even the right question to ask?



Hi @msankofa,

Currently, there is no way to do this within QIIME 2. However, you can externally run the
vsearch --fastq_join command as outlined in the vsearch manual available here, then import into QIIME 2. Note: merging reads is different than joining reads.

However, I suspect using such joined reads as input for denoising via deblur might not be appropriate . I say deblur, as feeding already joined / merged reads to DADA2 is inappropriate.

Also, you'll likely have issues with taxonomy assignment and phylogenetic reconstruction too, due to all the Ns.

Perhaps other can provide their insight. Otherwise, you should be fine to simply use only the forward reads.