I am trying to run the new MISeq SOP using Illumina data and I am not sure how to include all the fastq files from all my samples within the same command line. For example, if I have 12 fwd and rev fastq files, how do I include all of those files in the make.contigs command? Do I do this on a one by one fashion or do I create a batch command? I assumed I would be able to include all of the files at once, considering the fact that I’m including the .files file with the information for all of the samples.
Thanks!