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Question: Trinity with multiple datasets
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gravatar for j_deyarmin
19 months ago by
j_deyarmin • 0
j_deyarmin • 0 wrote:

Hello,

I am running trinity on 4 data sets (2 left reads, 2 right reads) and I want it to be compiled into one assembled transcriptome. Just be to be sure, I should be selecting multiple data sets, selecting my trimmed files, and then running it on those? Why does it parse it out into 4 jobs when doing this and not have one final job to compile them? Does trinity through galaxy do that automatically at the end?

Any help would be much appreciated.

Thanks!!
rna-seq • 626 views
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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by j_deyarmin • 0
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gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Trinity produces two datasets for every input. One output is a log file. The other output is the assembly result.

If using multiple data selections and two paired-end datasets are chosen, the Trinity tool is interpreting that input as two distinct assembly runs.

To run all of the sequence data in a single job, use the tool Concatenate to merge the left reads into one dataset, the same tool to merge the right reads into one dataset, then enter those results into the tool form as input.

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
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