Is there any other database (other than GEO datasets) to find RNA-seq data? I need the raw data thanks in advance.
•
written
by
biology_inform •
2 answers
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.
The NIAID Data Ecosystem allows you to search across dozens of repositories (including GEO, but about 40 others as well) to find RNA-seq data or other biomedical data: https://data.niaid.nih.gov/
You can use the interface to do a basic search and then it points you where to access the raw data from the source.
Log in to answer this question.
-
Datasets with RNA-seq and drug sensitivity data
written by octpus616 •
-
RNA-seq datasets with raw read counts for two group comparison
written by Ngrin •
-
similarity of transcriptome
written by biology_inform •
-
How can I find disease related RNA-seq data, where my gene of interest is differentially expressed?
written by richard.g.dale •
-
RNA-Seq analysis with Python
written by biology_inform •
-
How to select high quality RNA-seq datasets from SRA database?
written by harrypotterandsbt
-
Differential Gene Expression between 2 RNA seq groups without normal control
written by bionerd •
-
Total RNA RNA-seq database
written by lkmklsmn
-
Do specialized Hi-C databases exist?
written by svet.sidorov
-
Rna-Seq Data In Public Database
written by camelbbs
There are several tutorials that provide RNAseq for practice. You can download them, like here: https://github.com/griffithlab/rnaseq_tutorial/wiki/RNAseq-Data
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.