I am hoping to analyse a set of MiSeq fastq files using Mothur (16S V4 region). However I have run into a couple of issues which I think may be caused by the variation in read length in these files (10-250bp).
The fastq files were supplied to me after having been adapter and quality trimmed, but only reads shorter than 10bp have been removed. Is this a problem for make.contigs and downstream analyses? Is there a way to delete any short reads from these fastq files using Mothur?
Many thanks for any suggestions,