Question: RNA-Seq data avaliability online
0
gravatar for Qingyang Xiao
2.5 years ago by
Qingyang Xiao130
Stockholm
Qingyang Xiao130 wrote:

Hello, talents! As the title says, how to get RNA-Seq raw data(fastq format) of published researches is a big question for me. To my knowledge so far, I could only get raw data of array data in format of CEL file. from GEO dataset. Do you know how to get the fastq raw data so that I can do re-analysis?

sequencing rna-seq next-gen R • 1.1k views
ADD COMMENTlink modified 2.5 years ago by kristoffer.vittingseerup3.3k • written 2.5 years ago by Qingyang Xiao130
2
gravatar for kristoffer.vittingseerup
2.5 years ago by
European Union
kristoffer.vittingseerup3.3k wrote:

Most journals these days have it as a requirement that the raw (and more and more also processed) data is made publically available - it always say so in the article.

Most data ends op on geo but I have also seen some RNAseq end up on ArrayExpress (counterintuitive to the name).

There are a subset of studies where the raw data is protected (processed data is not) so you need to apply for access - those are typically at dbGaP with notable examples being GTEx and TCGA.

I've recently found that MetaSRA is a good way to search for studies you dont know about.

ADD COMMENTlink written 2.5 years ago by kristoffer.vittingseerup3.3k
0
gravatar for Arup Ghosh
2.5 years ago by
Arup Ghosh2.5k
India
Arup Ghosh2.5k wrote:

Just go to the SRA database (https://www.ncbi.nlm.nih.gov/sra/) and sear for datatype along with platform like Illumina Hiseq 2500.

ADD COMMENTlink written 2.5 years ago by Arup Ghosh2.5k
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