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Question: De novo transcriptome analysis pipeline
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gravatar for m_ko
17 months ago by
m_ko • 10
m_ko • 10 wrote:

Hello,

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 • 863 views
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modified 17 months ago by Jennifer Hillman Jackson ♦ 25k • written 17 months ago by m_ko • 10
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gravatar for Jennifer Hillman Jackson
17 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Tutorials for RNA-seq analysis in Galaxy are available here: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 17 months ago by m_ko • 10
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