Hello,

I am trying to download bigwig files for each sample of RNA-Seq data in GTEx via recount2. I can see bigwig file names defined for each sample (probably for each gene) in the 19th column through the following command. Then, how can I download the actual bigwig files in the column?

> download_study("SRP012682", type = "rse-gene")
> load(file.path("SRP012682", "rse_gene.Rdata"))
> colnames(colData(rse_gene))

Actually, the recount Bioconductor vignette stated that downloadstudy can be set with type="samples" that returns one bigWig file per sample in the study. However, downloadstudy cannot recognize this parameter value. In either way, can you please help me to download GTEx RNA-Seq bigwig files for each sample?

> url <- download_study('SRP012682', type=samples)
Error in type %in% c("rse-gene", "rse-exon", "rse-jx", "rse-tx", "counts-gene",  : 
  'match' requires vector arguments

Hi hyp15,

You can download the BigWig files for a study using download_study(project, type = "samples" ). Note that "samples" is quoted, unlike the one you provided in your code above.

So for example this works for downloading all the BigWig sample files for study SRP009615 (took 2 minutes for me).

download_study('SRP009615', type = 'samples')

Note that downloading all the BigWig files will use a lot of disk space (if you download them all it's about 8 TB).

Best, Leonardo

options(width = 120)
sessioninfo::session_info()
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