GEOfastq
can be installed from Bioconductor as follows:
The NCBI Gene Expression Omnibus (GEO) offers a convenient interface to explore high-throughput experimental data such as RNA-seq. GEO deposits RNA-seq data as sra files to the Sequence Read Archive (SRA) which can be converted to fastq files using fastq-dump
. This conversion process can be quite slow and it is usually more convenient to download fastq files for a GEO accession generated by the European Nucleotide Archive (ENA). GEOfastq
crawls GEO to retrieve metadata and ENA fastq urls, and then downloads them.
To get fastq data for a GEO series, we first retrieve the metadata for a GEO accession:
Next, we extract the sample accessions for this study and retrieve the GEO metadata and ENA fastq url for an example:
gsm_names <- extract_gsms(gse_text)
gsm_name <- gsm_names[182]
srp_meta <- crawl_gsms(gsm_name)
#> 1 GSMs to process
Now that we have retrieved the necessary metadata, we are ready to download the fastq files for this sample:
The following package and versions were used in the production of this vignette.
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