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Question: Trinity assembly multiple files
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gravatar for anna.kosakyan
8 months ago by
anna.kosakyan • 0
anna.kosakyan • 0 wrote:

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
trinity job assembly input dataset • 333 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by anna.kosakyan • 0
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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