I downloaded some 454 GS FLX Titanium 16S sequencing data using sratoolkit and the toolkit seems to work in general as I have succesfully converted the sra files into fastq files. But I have tried using sff-dump, my data is not supported while constructing formatter. According to the paper working with this data, they analyzed the data using mothur. So my question is how can I use fastq data in mothur?
Sorry, it’s been a while since we’ve done anything with 454 data and so the sra tools built in to mothur might not work as expected. The preferred approach to working with 454 data is to use the flow data from an sff file rather than from fastq files. Our 454 SOP can be found at: