So I’ve been haunted with the same problem as my reverse and forward fastq files have different lengths of sequences so that I can’t make.contigs. I took Dr. Pschloss’ suggestion to check for the “real” raw data, but they were the real ones. The sequencing data was from Mr.DNA. Normally we can deal with mixed forward and reverse reads by making contigs without oligo file then later trim.seqs with the oligo file. But this time one file has more sequences than the other one, which shouldn’t be the case even for Mr.DNA. We figured as long as we can extract the existing sequences and analyze data should be acceptable.
I uploaded the raw data and oligo file in google drive maybe someone would kindly take a look, please?