Hello everyone,
I am new to r-studio and I have to do differential gene expression analysis for my RNA seq data. Please tell me how should I start.I already have read counts for my samples.
Thank you
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written
by
rachana.cdri •
3 answers
Check out this tutorials,
http://www.gettinggeneticsdone.com/2012/09/deseq-vs-edger-comparison.html
OR
https://web.stanford.edu/class/bios221/labs/rnaseq/lab_4_rnaseq.html
Instead of DESeq you try DESeq2.
Dear Rachana,
I would suggest you to learn and understand the fundamentals of differential gene expression(DGE). Try to compile the following first :
- What is the objective of your study?
- What do you have as your data set, experimental setup, replciates, species in question, source of samples etc.
- Fundamentals of DGE - mapping, raw read counts, FPKM, RPKM or TPM.
A nice paper could be found here
Then, finally decide the appropriate tool; though all of them can more or less perform the basic analysis for you.
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Read about rnaseq here by University of Oregan. http://rnaseq.uoregon.edu/. Once RNAseq fundamentals are clear, try to reproduce this workflow as you are looking for differential gene expression: https://www.bioconductor.org/help/workflows/rnaseqGene/. R studio, as many people said here, is a R front end.
Could you update us with the method of obtaining read counts? (for eg featurecounts or htseq or any other tool).