Hi Kristen, Are these longer RNA sequences, such as transcripts? Then a tool like BLAT (or BLAST) would be a good choice. Both are wrapped for Galaxy and available in the Tool Shed for use with a local, cloud, or slipstream Galaxy. A cloud is probably the simplest choice for many users - and if the work is for research purposes, be sure to check out Amazon's grant program. http://usegalaxy.org/cloud http://usegalaxy.org/toolshed The public Main server at http://usegalaxy.org has mappers, but these are tuned for NGS reads. Other public Galaxy servers can offer mapping services, too. There are 50+ to review and what each offers changes over time. If you want to look, here is the list: https://wiki.galaxyproject.org/PublicGalaxyServers Keeping questions on the mailing lists helps us with tracking and is appreciated! https://wiki.galaxyproject.org/MailingLists Thanks, Jen Galaxy team https://wiki.galaxyproject.org/Support https://wiki.galaxyproject.org/BigPicture/Choices On 3/5/14 8:43 AM, Kristin Kernohan wrote:

Hi Jennifer

I am wondering if there is a way on Galaxy to align to the genome a file with many (~32000) fasta formatted sequences?

Thanks very much

Kristin

-- Jennifer Hillman-Jackson http://galaxyproject.org