Question

Which raw files (RNAseq) to download?

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AmyH • 0

@amyh-13117

Last seen 6.9 years ago

The Florey Institute of Neuroscience & …

Hello,

I am just getting started with processing mRNA data. I would like to use Bioconductor and R to analyse 12 different RNAseq datasets to look at differential gene expression (all analysed on Illumina HiSeq 2500).

I am stuck on the first step - which data files to download! This is the study I am interested in. Can anyone post some screenshots on exactly what links I need to click? Thanks for your help.

Amy.

bioconductor rnaseq • 2.4k views

ADD COMMENT • link updated 6.9 years ago by James W. MacDonald 65k • written 6.9 years ago by AmyH • 0

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You might also try recount:

https://jhubiostatistics.shinyapps.io/recount/

If your data sets are in there you can get them easily (already processed and easy to merge) using recount:

https://jhubiostatistics.shinyapps.io/recount/

ADD REPLY • link 6.9 years ago Jeff Leek ▴ 650

score 0 · Answer 1 · 2017-06-02

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chris86 ▴ 420

@chris86-8408

Last seen 4.4 years ago

UCL, United Kingdom

The files you are looking for are here:

http://www.ebi.ac.uk/ena/data/view/PRJEB14614

You can start with the .fastq files from the FTP.

ADD COMMENT • link 6.9 years ago chris86 ▴ 420

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Thanks chris86. What should I look for if the .fastq files are not available (e.g. some of the other datasets don't have .fastq available)

ADD REPLY • link 6.9 years ago AmyH • 0

score 0 · Answer 2 · 2017-06-02

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 11 hours ago

United States

An alternative is to use the SRA toolkit, which can be configured to use Aspera which will download data much faster than conventional FTP.

ADD COMMENT • link 6.9 years ago James W. MacDonald 65k

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Thanks James. That might be the best way for me to go, since all of my datasets are in SRA!

ADD REPLY • link 6.9 years ago AmyH • 0