Dear colleagues,
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.
Best wishes,
David
Where do you see this message?
Hi Bjoern,
The message appears in the output table after running Bowtie/TopHat in Galaxy. I was thinking of downloading the S. aureus genome again and re-uploading it to Galaxy to make sure there is no issue with the reference genome file.
Regards,
David
This is strange, can you share me your history?
Hi Bjoern,
Would it be best to share my colleagues details with you? That way you can look at the account history? If, so, how can I share this with you?
Regards,
David
Try with my username: bjoern.gruening@gmail.com
Glad Bjoern is examining. There may be a format issue triggering an index error. To double check, see the 'Troubleshooting' help here. Many fastq datasets can be corrected directly in Galaxy.
http://wiki.galaxyproject.org/Learn/CustomGenomes
Best, Jen, Galaxy team
Hi Bjoern and Jennifer,
I am actually performing this work for a colleague so I will ask her to share her history with you.
Thank you so much for your help
David