I'm looking at some 454 data (which I have little experience with) from https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-015-0101-x
Looking into microbial 16S analysis. This paper uses V3-V5, and apparently uses 454 for sequencing according to the SRA (for example, SRR048044). I have MiSeq data targeting the same locus with overlapping ends to create merged reads.
As a newcomer to 454 I have a few questions:
1) 454 is probably processive, and my impression is that reads beyond the theoretical length are probably just errors. Some reads in the fastq come back as almost 1000 nt long, which is longer than expected. The quality score crashes to well below ten after 500-600 nt, so my guess is that the sequences generated beyond a given length are just noise?
2) Additionally, is the difference in chemistry and Q-score calculation going to adversely effect a direct comparison of OTU's generated in both platforms?