I am trying to assemble my reads and also remove primers/barcodes etc. I used primers 515f (GTGCCAGCMGCCGCGGTAA) and 806r (GGACTACHVGGGTWTCTAAT) and index primers. How should I set up the oligos file such that the primers and barcodes are removed? Nothing I do seems to be working.
Also want to mention that these reads are already demultiplexed!
Here’s a link to the oligos file page, http://www.mothur.org/wiki/Oligos_File. Since the barcodes are in the index file and the primers need to be removed here is the setup you are looking for.
primer GTGCCAGCMGCCGCGGTAA GGACTACHVGGGTWTCTAAT
barcode forwardIndexBarcode reverseIndexBarcode barcodeName
forwardFastqFile reverseFastqFile forwardIndexFile reverseIndexFile
mothur > make.contigs(file=file.txt, pdiffs=2, bdiffs=1)
NOTE: If you are missing an indexed barcode you can indicate it by using the keyword NONE.
ie. barcode forwardIndexBarcode NONE barcodeName