Rna-seq data

Question

[biology_inform]

Is there any other database (other than GEO datasets) to find RNA-seq data? I need the raw data thanks in advance.

[cpad0112]

There are several tutorials that provide RNAseq for practice. You can download them, like here: https://github.com/griffithlab/rnaseq_tutorial/wiki/RNAseq-Data

[ATpoint]

You can browse thousands of datasets for raw counts via https://bioconductor.org/packages/release/bioc/html/recount.html though some details on why the thousands of datasets at GEO are not suitable would help to provide a better answer.

Answer 1

[Mitra]

Besides SRA/GEO from the NCBI,

you have ENA (https://www.ebi.ac.uk/ena/browser/home) which is the European database hosted by the EMBL-EBI.

I personally prefer to navigate the data in the ENA through the other service: ArrayExpress (https://www.ebi.ac.uk/arrayexpress/browse.html) which was originally for microarrays but allows to browse for RNAseq studies too. Another pro of using ArrayExpress is that you can see right from the search page if there are raw (Fastq files) and processed files (e.g. bam files) for a given study.

Many datasets will be found in both databanks but not all, so it is worthwhile to have a look at both.