Question: Example datasets for RNA-Seq Differential Expression Analysis
0
gravatar for AntonioParra
6 weeks ago by
Seville
AntonioParra0 wrote:

Hi! I'm just started to learn about differential analysis expression gene on R, but I don't know where can I find some datasets of raw counts and metadata (samples info) from RNA-Seq for perform some tests, or if there are any library in R 3.5.2 which contain any example dataset (I've tryed with some libraries like 'airway', but that package is not avaiable in R 3.5.2 version). Any suggestions? Thank you so much.

rna-seq R • 235 views
ADD COMMENTlink modified 6 weeks ago by HG1.1k • written 6 weeks ago by AntonioParra0

If you are planning to use DESeq2 then it refers to a test dataset you can use ("pasilla" data). Here is the detailed vignette for DESeq2.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax65k
1
gravatar for Buffo
6 weeks ago by
Buffo1.5k
Buffo1.5k wrote:

Hi Toño, if you write RNAseq on pubmed you will get lots of papers where you can get access to raw reads such as: sequence read archive (SRA).

ADD COMMENTlink written 6 weeks ago by Buffo1.5k
1
gravatar for husensofteng
6 weeks ago by
husensofteng60
Stockholm, Sweden
husensofteng60 wrote:

If you are looking for any dataset for testing purposes, I think the easiest way is to go the encode project and click on any assay type. Here is an example page browse further down the page and click on File Details to get the list of files that you can download directly.

Another basic web tool that would allow you to get downloadable links from SRA is: SRA Explorer You just have to enter a search term and add the desired results to the basket. Clicking on the Accession link takes you to the study page where you get more info about the dataset.

The nice thing is that it provides direct links to download fastq files from NCBI's SRA ftp server. For an example, just copy and paste the link to a web browser, however for downloading many files use the other provided scripts.

Alternatively, for downloading large sets or in a more automated way you could use the SRA toolkit.

ADD COMMENTlink written 6 weeks ago by husensofteng60
1
gravatar for HG
6 weeks ago by
HG1.1k
Germany
HG1.1k wrote:

You can download test data from "The Griffith Lab"

https://github.com/griffithlab/rnaseq_tutorial/wiki/RNAseq-Data

there's also a nice tutorial available.

ADD COMMENTlink written 6 weeks ago by HG1.1k
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