Hi guys! I’ve recently switched to a newer sequencing company offering good price and good depth of amplicon sequencing using the Illumina pe2500. As I’m starting a new batch of experiments I’ve been struggling with choices of region to sequence, I opted for the v3v4 (338f - 806r) to try out, the extra length up from v4 would be great if 2x250 is sufficient for most reads to merge, which was my biggest concern but the company assured me it would be fine and its a standard region to use with the pe2500. I’ve just received the results today, and the quality looks surprisingly good, actually unbelievably good from my understandings, thats why I’m here asking. Does this look normal?
This is the demux-summarize result of the fastq file with adapters trimmed, looks like theres no need for hard trimming at all? From my previous experiences using Illumina products they usually look more like this:
Am I just outdated and worrying too much or does it look reasonable? Any suggestions are appreciated, thanks!