Running into a weird problem I’m helping to trouble shoot. We have a run which may have some technical issues, which we are re-running, but wanted to see if we could use only the forward reads to de-multiplex and annotate.
Essentially, the forward and reverse runs are in fastq files and the barcode is in another fastq files. I realized that since the barcode is not in the sequence itself it is not useful if I use cutadapt. The forward read/reverse read fastq/barcode fastq have been performed through the EMP protocol. Illumina MiSeq.
did you import as paired-end already? demux emp-single can actually operate on EMPPairedEndSequences artifacts and will only use the forward reads, so that is one possibility. If your data are multiplexed I am assuming it is an EMP format.
Excuse my dumb question. . . But if I decide to import forward reads only, is it essentially running single - end data?
What if I run the forward and reverse reads separately, both as single - end data? Providing the quality of both are closely related, would I potentially get similar results? (w single fwd vs single rev)
I ran forward reads as single recently and got 2x the amount of features present (maybe more) in each sample.
(the V4 primers used are 515f + 806r, so look at those positions on this plot)
Higher entropy is a good thing. It means that you are more likely to be able to differentiate those species based on that sequence. Lower entropy = less likely to differentiate species (more likely to get classification at family level and below, and likely to get fewer ASVs/OTUs, yielding lower sensitivity for differentiation of sample groups)