Question: DGE using trinity
0
gravatar for loly.pearl86
3.5 years ago by
loly.pearl8620
Australia
loly.pearl8620 wrote:

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, assemblu uding de no vo , 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 commandline?!!

 

Thanks

 

 

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ADD COMMENTlink modified 3.5 years ago by Antonio R. Franco4.0k • written 3.5 years ago by loly.pearl8620
0
gravatar for Antonio R. Franco
3.5 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:
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
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Antonio R. Franco4.0k

Thanks for u reply 

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

 

thanks

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by loly.pearl8620
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