Single end read processing

Hi, I am a postgraduate student and I want to learn about processing SINGLE END reads using mothur. And I have visited most of the forum comments and I find them difficult to understand. Can anyone post or direct a protocol where I can learn about processing Illumina SINGLE END reads using mothur?

Hi Rahul,

I’d suggest looking at the 454 SOP and how we use quality scores to process data and adapt that to the MiSeq data you have. Is there a reason you only have a single read? I would strongly discourage using single reads as the quality is going to be very poor relative to paired sequencing.


thanks for your reply, sir. The study objective is to compare the microbial diversity in a particular place using already publish publically available datasets. One of the studies has SINGLE end read and that’s the reason why I want to process. I will look into the 454 SOP for that matter. thanks again for your help, sir.

Considering what you said:

If you would like to mix single and pair end datasets in a single analyses, one possibility is doing a very strict QC of the single-end using other software (e.g. MEFIT or similar), and then create the RC of your curated fastq files, and feed them to mothur as the R1-R2 pairs of a pair-end… But, if you do it, use very very very high quality thresholds in your first step, since mothur will likely take them all as perfect.

Pat might be choking after reading this, though. : )