MiSeq fastq files, short read lengths


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,


Get the raw, untrimmed data and start over. I can guarantee you that you know more about handling these data than whoever trimmed them. :slight_smile: