I am very new with Illumina sequencing and also with Mothur. I just received my sequences back from the sequence facility after being run in Miseq. They sent me four files:
- Index file: Undetermined_S0_L001_I1_001.fastq.
- R1: Undetermined_S0_L001_R1_001.fastq
- R2: Undetermined_S0_L001_R2_001.fastq
- mapping file with barcodes with the header: #SampleID BarcodeSequence LinkerPrimerSequence Description
I know I have to demultiplex but I am not sure if there is a command in Mothur. I think it could be done with trim.seqs, but I am not sure how my oligos file should look like. I donÂ´t really understand what the index file means.