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:
data_dir <- tempdir()
# example using smaller file
srp_meta <- data.frame(
run = 'SRR014242',
row.names = 'SRR014242',
gsm_name = 'GSM315559',
ebi_dir = get_dldir('SRR014242'), stringsAsFactors = FALSE)
res <- get_fastqs(srp_meta, data_dir)
#> Warning: Failed to connect to ftp.sra.ebi.ac.uk port 21: Timed out
The following package and versions were used in the production of this vignette.
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows Server x64 (build 17763)
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#> [2] LC_CTYPE=English_United States.1252
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#> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United States.1252
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] GEOfastq_1.1.0
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#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.6 knitr_1.33 magrittr_2.0.1 doParallel_1.0.16
#> [5] R6_2.5.0 rlang_0.4.11 foreach_1.5.1 stringr_1.4.0
#> [9] plyr_1.8.6 tools_4.1.0 parallel_4.1.0 xfun_0.23
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#> [17] digest_0.6.27 sass_0.4.0 bitops_1.0-7 codetools_0.2-18
#> [21] RCurl_1.98-1.3 evaluate_0.14 rmarkdown_2.8 stringi_1.6.2
#> [25] compiler_4.1.0 bslib_0.2.5.1 jsonlite_1.7.2