I have downloaded a bunch of 16S sequence data sets from NCBI in SRA format. I have used NCBI SRA toolkit to convert them into fastq format for further analysis with mothur. When try to merge the both R1 and R2 fastq files by using make.contig command, i am getting this following error.
“St_3_1M_young_sound_2015.1.1 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.”
When i use my own dataset for merging i never had any issue. Can some one assist me, how to rectify this issue.