RNA-seq Replicate papers for beginner

Question

[layan.essam]

I have a good R and statistical analysis background (also with machine learning). in addition, I'm a fresh biotechnology grad. I would like to try to replicate some Rna-seq analysis with R papers (with their provided data). Any SHORT (beginner-friendly) papers to recommend?

Answer 1

[ATpoint]

I would not right jump into any dataset but rather start with guided tutorials to get the concepts right and most importantly learn a good quality control. There are papers, most recently one that claimed that standard tools like edgeR and DESeq2 underperform in certain situations, where the entire claim could be falsified as it turned out authors simply skipped QC entirely and did not take into account the big batch effect in their dataset.

But back to the question, there is the:

123RNAseq tutorial, that is mainly focussed on edgeR and limma

• https://bioconductor.org/packages/release/workflows/html/RNAseq123.html
• https://bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html

The Bioconductor gene level workflow and the DESeq2 vignette, that is DESeq2 obviously:

• https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
• https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

What I find excellent as well are the tutorials from HBC, they offer lots of background information and have different topics, e.g.

• https://hbctraining.github.io/main/#current-topics-in-bioinformatics-series
• https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html

Edit: I saw that someone at StackExchange suggested Galaxy for that question. Don't use Galaxy, there is not much learned from using these kinds of fixed frameworks where you only have to press some buttons. I encourage to really look at the data, explore the different functions and options the packages have first hand by interacting with them in R natively.

[layan.essam]

thank you so much for your help, I appreciate it. I forgot to mention I already did a lot of guided tutorials and exercises. so I wanted to see the full picture and do a full project to present in my portfolio for an entry-level job. so if u know any good papers for the purpose (beginner-friendly) will be of much help.