mRNA expression Count

Question: mRNA expression Count

17 months ago by

anshulmbi • 10 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

differential rna-seq expression htseq_count • 670 views

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modified 13 months ago • written 17 months ago by anshulmbi • 10

17 months ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 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 COMMENT • link written 17 months ago by Mo Heydarian ♦ 830

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 REPLY • link written 17 months ago by anshulmbi • 10

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 REPLY • link written 16 months ago by Mo Heydarian ♦ 830

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 REPLY • link written 16 months ago by anshulmbi • 10

13 months ago by

anshulmbi • 10

anshulmbi • 10 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 COMMENT • link written 13 months ago by anshulmbi • 10

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 REPLY • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

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