Forum:Find a research paper for reproducing the results

Question

[grant.hovhannisyan]

Hi Biostars,

For some classes I need to find a simple reseach paper which can be reproduced by students. The paper basically should use RNAseq data to compare 2 (or whatever) conditions, find dif. expressed genes and perform GO term enrichments, so basically the standard pipeline - fastqc > trimmomatic > STAR > DEseq2 > clusterprofiler (or any popular derivitive of this pipeline). I was searching for quite some time but didn't find anything simple enough, so any suggestions would be greatly appreaciated.

cheers

[GenoMax]

Try and find data/tutorials that are used by cores to teach data analysis. These should be well whetted. Here is one example from Babraham in UK: https://www.bioinformatics.babraham.ac.uk/training.html#rnaseq

Answer 1

[Mensur Dlakic]

There are numerous papers in Nature Methods, and especially in Nature Protocols, that have step-by-step guidelines that should be reproducible. Two fairly broad lists can be obtained by clicking on links below, and from there you will have to narrow it down on your own.

https://pubmed.ncbi.nlm.nih.gov/?term=nat+methods%5Bjo%5D+rna+seq https://pubmed.ncbi.nlm.nih.gov/?term=nat+protoc%5Bjo%5D+rna+seq

Answer 2

[Jeremy Leipzig]

I would throw in SRA as a search term just to make sure you have open data. If you are dead set on a reproduction (as opposed to a refactor), you'll want to add "github" as a search term as well.

https://www.lens.org/lens/search/scholar/list?q=(SRA%20deseq2%20%22Gene%20Ontology%22)&p=0&n=10&s=_score&d=%2B&f=false&e=false&l=en&authorField=author&dateFilterField=publishedYear&orderBy=%2B_score&presentation=false&preview=true&stemmed=true&useAuthorId=false