I have paired end Illumina Miseq data. So I am following the MiSeq SOP, which is really well done and easy to follow, by the way. In contrast to the SOP, my sequences are already assembled (by the sequencing company) in contigs, so I don’t have to do the fist step (make.contigs). As a consequence I however don’t know how to get the group file and the renaming of the fastq (converting : to _). Up to now I did it with make.group, I the merged the fastq to one fastq with merge.files. If I then don’t convert the fastq to a fasta I have problems when looking for unique sequences. If I however make a fasta the group names don’t fit the sequence names any more. I can avoid this by first converting all the fastq to fasta, before making the group. Up to now I did all of this with small batches but now I would like to work with all my samples which are more the 100. As far as I am concerned I can not make fastq.info for multiple files, so I would have to do that too many times, and also to make the groups I have to write all the sample names and group names by hand, which takes very long.
I am sure there is a super short and easy solution to my problem, using something corresponding to the stability.files in the SOP, but I just can’t find out how to do that without make.contigs..
Thanks for your help.