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