Dear Galaxy team, I am trying to assemble 12 paired reads at the same time using Trinity on Galaxy. I use multiple file option, but in the result it creates 12 separate assemblies. Does Galaxy has such an option to create one big assembly from multiply files? Many thanks Anna
Yes, when given multiple inputs, a separate job is created for each pairing.
To run all of the data in a single assembly, use the tool Concatenate to put all of the forward reads into a single fastq dataset, then do the same for the reverse reads.
Collections/datasets could be also be combined into merged datasets using the tool Collapse Collection. If interested, this is how: https://galaxyproject.org/tutorials/collections/
Should that larger job, later on, fail for a memory error, then it is too large to run at Galaxy Main https://usegalaxy.org. https://galaxyproject.org/choices/#which-option-to-choose
Thanks, Jen, Galaxy team