I’m trying to separate data from a barcoded MiSeq run into separate groups. The sequencing service I’m using used barcodes on the forward primer only, and I made an oligos file with the barcodes and primers (below).
When I run the make.contigs command (using fasta=stability.files and the .files file has the three columns as described in the MiSeq SOP wiki) I get an error that says “barcodes must be paired unless you are using an index file.” I’ve searched though all the files I have, but I can’t find anything that looks like the example index file on the make.contigs wiki page. Is this something I’m meant to make? If so, can someone elaborate on how?
Thanks! Let me know if you need more information!
Eric
I’ve continued going through files and found something that looks very similar to the example index file, but it’s not fastq, the sequences are much longer than in the example, and the header isn’t in the same format (first few lines pasted below). The first 8 bases do correspond to my barcodes, but I’m not sure if this is my index file or if it somehow becomes my index file.
Dear Mothur,
I am getting more of scrap sequences than contigs. I guess the problem could be oligos file. Please find it below
mothur “#make.contigs(ffastq=F_001.fastq, rfastq=R_001.fastq,oligos=exp1.oligos, processors=1)”