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DGE using trinity

Hi everyone,

I am doing gene expression study for 2 different treatments in order to comparing them and I follow this methods:

RNA extraction,sequencing by illumina ,QC, trimmomated, assembly using de novo, CEGMA, then I start Differential Expression Analysis Using a Trinity Assembly in command line following this steps:

  • Alignment-based abundance estimation methods
  • Build Transcript and Gene Expression Matrices
  • Counting Numbers of Expressed Transcripts or Genes(no biological replications)

Now I want run Extracting and clustering differential expressed transcripts but not sure should I do TMM normalisation before or no?! if yes How can I do TMM normalisation using trinity in command line?!

Thanks

assembly alignment
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updated by Ram Ram • written by loly.pearl86 • loly.pearl86

1 answer

I believe you use Trinity only to assemble a transcriptome to use as reference for mapping your reads with programs such as tophat, BBmap, star, kallisto an others After mapping you count reads with RTSeq-Count or alike, and then process an normalize the data with packages such as DESeq2, NOISeq, edgeR, etc
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written by Antonio R. Franco Antonio R. Franco

Thanks for u reply

Yes this what I did but I stick now in this step How can I do normalization?

thanks

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updated by Ram Ram • written by loly.pearl86 • loly.pearl86

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