Hiya, I'm trying to make contigs in mothur (v.1.41.1) from my mrDNA-sequenced samples. I've used MrDNA:s Fastq Processor program to get the reads indexed, and made file with mothur make.file command. Everything looks ok at this point, however, I don't have the same number of reads in forward and reverse, as FastQProcessor result.file tells me. For example, Barcodes R1 Seqs R2 Seqs ATTCCGAC 37762 34504
Therefore, when I try make.contigs using the file file, I get an error message "xxx is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding." and mothur crashes because of a segmentation fault.
I've been trying to find a solution by reading help forums, and remove.seqs could be the answer, but I don't understand how to use the command to remove unpaired reads from both R1 and R2. The reads are at this point in fastq-format. Cheers, Lotta