splitting fastq files


I have a single fastq file from an Illumina HiSeq run that includes several multiplexed samples, with the ID tag run right next to the forward primer so that it is in my sequences. However, I need to separate it into individual fastq files, one for each multiplexed sample, for submission to the SRA. Although, I don’t want any other trimming, fasta formation, etc. to take place because I need to submit raw fastq files.

Is there a way to do this in mothur? I was not able to find a method on the forums. And I can’t figure out a way to do it via trim.seqs or make.contigs, since these operate on fasta files and don’t generate new qual files so that I can go back and rejoin them using make.fastq. Am I missing something? Thanks very much!

The fastq parameter will be added to the list.seqs, get.seqs and remove.seqs commands in version 1.33.0. This will help you select sequences by name from fastq files.