I am trying to find a way to split my reverse and forward fastq files into groups according to the barcode combinations. Right now all of the sequences go into the scrap.contigs.fasta file, but when I open that up I can find my primers and barcodes. I’ve used the fastq files before in another custom perl workflow to strip the primers/barcodes and make the fasta files, so I am wondering why I can’t get this to work.
The error message in .scrap.contigs is ‘bf’
Working with mothur 1.33.3
make.contigs(ffastq=Thorn-Funagl-2_S1_L001_R1_001.fastq, rfastq=Thorn-Funagl-2_S1_L001_R2_001.fastq, oligos=TG_r3.oligos, tdiffs=2, processors=4)
Using the oligos file formatted for paired end sequencing:
primer AACKGCGAGTGAAGMGGGA TCTTTCCCTCACGGTACTTG 28S
barcode ATAACTAA TCCTTTCT TG1X
barcode ATAACTAA CATTAATT TG2X
barcode CATTAATT AATATTTT TG3X
barcode CATTAATT TATTATAT TG4X
barcode CATTAATT TCCTTTCT TG5X
barcode CATTAATT CATTAATT TG6X
barcode TTTCTTCT AATATTTT TG7X
barcode TTTCTTCT TATTATAT TG8X
We had used the adapter-nnnn-barcode-primer format for our runs, so the files do start with 4-5 bases before it gets to the barcode. I don’t know if that will cause a problem.
Thanks for your help!