Basic adapter trimming question - MiSeq

[microgirl123]

Hi, I'm new to next-gen sequencing and we have a nice, new MiSeq. Although, I've seen the post about not using adapter trimming on the MiSeq I think our customers might want to. We're mostly just doing PCR amplicons (not human) and bacterial resequencing and assembly. How do I know if adapter trimming needs to be done? Any information about adapter trimming would be great! I'm pretty good with the basics of how to run the MiSeq but hazy on the software/bioinformatics ends of things!

[ECO]

Search and read some more. Assuming you're using "standard" adapters and library prep, you should trim adapters if a significant portion of your inserts are shorter than your read lengths (thus reading into the distal adapter).

Also, if you're sequencing amplicons, you should certainly trim out (or at least be aware of), the primer sequences as they are entirely sequence of synthetic DNA.

[microgirl123]

Thanks ECO! This whole first run has been a learning experience/problem. When the MiSeq was installed and I was trained we only had the v1 chemistry. Now that we have the v2 chemistry (but not the hardware update), my inserts are too small. So I had only ~200-300 bp inserts but did 2x250 reads. I think this probably led to me reading into my adapter in some cases. I also had a huge hangup with the Velvet assembler because of the massive overlap in reads!