Hi, thank you for help in advance. I have say 50 samples, with multiple pairs of FASTQ files for each sample. My questions are:
- Can I process 50 samples separately in mother following the MiSeq SOP? I mean, can I run 50 separate jobs for 50 samples? I think I can do so if there are no steps in mothur where reads from different samples are pooled (like the GATK use pooled reads to call variants sites).
- For one sample that has say 5 pairs of fastq files, can I run make.contigs 5 times for each pairs of FASTQ files to use 5 CPU cores at the same time? If yes, how can I merge them later?
Thanks a lot.
Fan