Danielle Lema posted a comment on discussion Bowtie Help

I ran bowtie 2 against a reference genome and it worked perfectly. After saving the data to external, I deleted the paired-end reads from my hpc directory. Later, we decided to align reads against the mito-genome, so I uploaded the same exact files to my directory, and running the exact same command on the exact same files (but with different reference), I got the error " Error, fewer reads in file specified with -2 than in file specified with -1" I know the files have the same number of reads because...