The best practive depends on whether you expect the reads to overlap or not. What is the ratio of your read length to your expected insert size? If the reads do not overlap, you should concatenate the FASTQ files and send the merged file to MG-RAST. If the reads do overlap, you should merge the mate pairs (for instance, Hammingaligner from illumina does this) and upload the merged reads. William Trimble --for the MG-RAST team. On Mon, Aug 8, 2011 at 11:05 AM, <[email protected]> wrote:

How should we upload illumina pair-end data? Both fastq files? Cheers David.