I am currently trying to aligning reads from a dual RNA-seq experiment to the Staph aureus genome. For this, we have dowloaded the S. aureus reference genome in FASTA format from NCBI and stored in our history. We then have selected this genome from the history (with the correct attributes assigned) as the reference for our alignments using both Bowtie and TopHat. However, after the run is completed we received the following message with no accompanying results:
Settings: Output files: "genome.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default
Can anyone tell us where we are going wrong and if there is anyway we can correctly align our reads to the Staph aureus genome.