I ran Trinity for RNA seq assembly yesterday. It has been gone for nearly 24 hours but is still operational. Could you please tell me if Trinity is operational in galaxy Euorpe?
Hi @Md_Atiqur_Rahaman,
run time depends on amount of data, quality and resources allocated for the job, and some Trinity assembly take long time. Also, sometimes Galaxy does not refresh history panel, so completed jobs are displayed as running. Click at Galaxy Europe banner in the top left corner to refresh the web page and refresh the history. I don’t know the current wall time for Galaxy Europe, but in they we very generous in the past. You may also consider alternative tools, like rnaSPAdes.
Kind regards,
Igor
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Thanks . I ran 100 gb data .Could you give me rnaSPAdes hands script ?
@Md_Atiqur_Rahaman,
100 GB is a lot of data, and with the default settings Trinity will run digital normalization before the assembly.
I have not used rnaSPAdes on command line and have very limited experience with the software. It is available on Galaxy Europe, just paste rnaSPAdes into Filter/Search box at the top of the tool panel.
Kind regards,
Igor
Thanks for your valuable suggestions.