Question: De novo transcriptome analysis pipeline
gravatar for m_ko
16 months ago by
m_ko10 wrote:


I am currently running Trinity to do de novo transcriptome assembly of a breeding gland from a frog Hymenochirus boettgeri to find a pheromone sequence and was planning on running Salmon after to quantify. What other tools of Galaxy are recommended for transcriptome annotation? Thank you.

rna-seq • 774 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by m_ko10
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Tutorials for RNA-seq analysis in Galaxy are available here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 16 months ago by Jennifer Hillman Jackson25k

I have not been able to get Salmon to work for the past four days. Following the instructions of a previous post, I deleted the old jobs and I have been starting new ones for the past few days but they remain on queue and do not progress.I tried it with the test datasets provided by Salmon and it worked fine in a few minutes. I do think the problem is that my files are too large. The reference transcriptome is Xenopus (2.6GB) and my transcriptome from Trinity is 295.9 MB. Is there a different route that is recommended to quantify the transcriptome from Trinity?

ADD REPLYlink written 15 months ago by m_ko10
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