Question: mRNA expression Count
1
gravatar for anshulmbi
5 months ago by
anshulmbi10
anshulmbi10 wrote:

Hi, I want to get mRNA expression count from RNA-Seq data. I am able to get gene expression count from HTSeq Count tool available in Galaxy. Please help me for mRNA expression. Thanks

ADD COMMENTlink modified 6 weeks ago • written 5 months ago by anshulmbi10
0
gravatar for Mo Heydarian
5 months ago by
Mo Heydarian790
United States
Mo Heydarian790 wrote:

Hello, You can perform RNA-seq analysis in Galaxy. Most of the standard tools for RNA-seq analysis are available on useGalaxy.org

Please have a look at the following tutorial that has step-by-step instructions for dealing with RNA-seq data, including sample data for trial and error: https://galaxyproject.github.io/training-material//topics/transcriptomics/tutorials/de-novo/tutorial.html

Hope this helps! good luck with your analysis!

Cheers, Mo Heydarian

ADD COMMENTlink written 5 months ago by Mo Heydarian790

Hi, Mo Heydarian I am very grateful to you for your valuable suggestion.

I want to get mRNA expression count with mRNA accession number.

Please help me for the same. Anshul

ADD REPLYlink written 5 months ago by anshulmbi10

Please follow the tutorial I provided. In the tutorial normalized counts of transcripts are generated by DESeq2.

You will need to provide the reference transcriptome (GTF) corresponding to your the organism you are working with: https://genome.ucsc.edu/cgi-bin/hgTables

Thanks for using Galaxy!

Cheers, Mo Heydarian

ADD REPLYlink written 5 months ago by Mo Heydarian790

Hi, Mo Heydarian

Thanks for your expert suggestions. I tried your suggestions, but when I want to upload customized transcriptome in GTF format on galaxy it showing error and the same problem with your database (as you mention in the tutorial). How can I troubleshoot this problem? Thanks!!

Anshul

ADD REPLYlink written 5 months ago by anshulmbi10
0
gravatar for anshulmbi
6 weeks ago by
anshulmbi10
anshulmbi10 wrote:

Hi, Mo Heydarian

I have mRNA expression count from RNASeq data with the help of feature count. I want to normalize these expression count, I have idea how to normalize the qPCR data but no idea how normalize RNAseq data, is the same process or any difference.

Please help me in this regard.....

Thanks...

ADD COMMENTlink written 6 weeks ago by anshulmbi10

Use FeatureCounts's Advanced options to customize the rules for calculating counts.

For RNA-seq differential expression normalization, how-to is covered in this tutorial: https://galaxyproject.org/tutorials/nt_rnaseq/

All tutorials: https://galaxyproject.org/learn/

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Jennifer Hillman Jackson23k
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