Question: No Cufflinks data
0
gravatar for m_ko
7 months ago by
m_ko10
m_ko10 wrote:

Hello,

I have been trying to use Cufflinks for my files from FasqToSam but I I have not been able to get any data from Cufflinks (the data is marked "empty" or "1 line". Is this a format issue or something else? Thank you!

cufflinks • 225 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by m_ko10
0
gravatar for Mo Heydarian
7 months ago by
Mo Heydarian790
United States
Mo Heydarian790 wrote:

Hello,

Can you provide some more information on your pipeline? Did you map your reads to a genome?

Please have a look at the tutorials here for recommended pipelines to use for RNA-seq analysis: http://galaxyproject.github.io/training-material/topics/transcriptomics/

Thanks for using Galaxy!

Cheers,

Mo Heydarian

ADD COMMENTlink written 7 months ago by Mo Heydarian790
0
gravatar for m_ko
7 months ago by
m_ko10
m_ko10 wrote:

I ran my RNA sequencing data through Trinity for de novo transcriptome assembly. I am currently running Tophat for my samples because the files from Trinity could not be read by Cufflinks. My organism is a frog called Hymenochirus boettgeri, related to Xenopus, and I want to do transcriptome annotation to find a gene sequence of a pheromone from the breeding gland of the frog. I took a look at the pipelines provided in the link and they did not use Trinity as part of it. Are there any pipelines you recommend that use Trinity? Also, my samples were sent to FGL of QB3 Berkelely. Is the quality control step still necessary? Thank you so much.

ADD COMMENTlink written 7 months ago by m_ko10
0
gravatar for Mo Heydarian
7 months ago by
Mo Heydarian790
United States
Mo Heydarian790 wrote:

Hello,

Trinity will output transcript sequences in fasta format. You can use these sequences as a reference for tools to quantify transcript expression levels. Perhaps you could try using Salmon to quantify expression levels.

You should always do QC on your samples.

Good luck hunting for your pheromone!

Cheers, Mo Heydarian

ADD COMMENTlink written 7 months ago by Mo Heydarian790
0
gravatar for m_ko
7 months ago by
m_ko10
m_ko10 wrote:

Thank you for the reply.

Is the pipeline for De novo transcriptome reconstruction with RNA-seq applicable to Trinity or is there another pipeline that is more suitable? I have not been able to find one for it. Thank you again! :)

ADD COMMENTlink written 7 months ago by m_ko10
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