Rna-seq data
1
0
Entering edit mode
2.7 years ago

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

data rna-seq • 768 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
2.7 years ago
Mitra ▴ 10

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2100 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6