I have a question regarding the mapping of RNA-seq data. I am hitting a wall, because some of my jobs keep getting terminated due to run time.
“This job was terminated because it ran longer than the maximum allowed job run time.”
I am using the default settings of Tophat (for Illumina) and the FastQ files are in the 4-7 Gb range. I get this error after about 48h of jobtime. I wonder if there is any way to circumvent this (like extending the allowed run time) that does not involve installing Galaxy locally.
Thanks for your help!