My samples are a mix of 16S and ITS amplicons (only 16S or only ITS in one sample, but all sequenced together). I began bioinformatics on all fastq files as I intend on running the same commands on all samples up until align.seqs where I want to skip this step for ITS samples. Is there a way of separating my samples before align.seqs?
Might be a more elegant solution, but this is something I’ve used in the past and it worked fine in my instance.
Provided your primer sequences are still intact you can use pcr.seqs with an oligos.file targeting your 16S sequences and cull the unwanted (ITS) reads that way. Could try the inverse for ITS.
Thanks for the suggestion but I’ve done a shotgun approach and therefore my primers are definitely not in all my reads.
Hi - you could blast your sequences against reference 16S and ITS sequences to find which sequences are which and then split out the data. There isn’t something directly in mothur to do this.