how to download bigwig from recount2?
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hyp15 • 0
@hyp15-21655
Last seen 19 months ago

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
recount • 337 views
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@lcolladotor
Last seen 12 days ago
United States

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

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[1] D:/Documents/R/win-library/3.6
[2] D:/R/R-3.6.1/library
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download_study('SRP009615', type = 'samples')
2019-08-15 15:25:04 downloading file SRR387777.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'text/plain; charset=UTF-8' length 94700336 bytes (90.3 MB)
downloaded 90.3 MB

2019-08-15 15:25:15 downloading file SRR387778.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw'
Content type 'text/plain; charset=UTF-8' length 107837710 bytes (102.8 MB)
downloaded 102.8 MB

2019-08-15 15:25:28 downloading file SRR387779.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw'
Content type 'text/plain; charset=UTF-8' length 97582496 bytes (93.1 MB)
downloaded 93.1 MB

2019-08-15 15:25:38 downloading file SRR387780.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw'
Content type 'text/plain; charset=UTF-8' length 95744851 bytes (91.3 MB)
downloaded 91.3 MB

2019-08-15 15:25:50 downloading file SRR389077.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw'
Content type 'text/plain; charset=UTF-8' length 66256981 bytes (63.2 MB)
downloaded 63.2 MB

2019-08-15 15:25:57 downloading file SRR389078.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw'
Content type 'text/plain; charset=UTF-8' length 78183706 bytes (74.6 MB)
downloaded 74.6 MB

2019-08-15 15:26:06 downloading file SRR389079.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw'
Content type 'text/plain; charset=UTF-8' length 127788534 bytes (121.9 MB)
downloaded 121.9 MB

2019-08-15 15:26:20 downloading file SRR389080.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw'
Content type 'text/plain; charset=UTF-8' length 87858929 bytes (83.8 MB)
downloaded 83.8 MB

2019-08-15 15:26:29 downloading file SRR389081.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw'
Content type 'text/plain; charset=UTF-8' length 79387326 bytes (75.7 MB)
downloaded 75.7 MB

2019-08-15 15:26:38 downloading file SRR389082.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw'
Content type 'text/plain; charset=UTF-8' length 63161568 bytes (60.2 MB)
downloaded 60.2 MB

2019-08-15 15:26:46 downloading file SRR389083.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw'
Content type 'text/plain; charset=UTF-8' length 69695346 bytes (66.5 MB)
downloaded 66.5 MB

2019-08-15 15:26:54 downloading file SRR389084.bw to SRP009615/bw
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw'
Content type 'text/plain; charset=UTF-8' length 67003461 bytes (63.9 MB)
downloaded 63.9 MB


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Thank you very much Leonardo Collado Torres!

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Hello,

because GTex is that big, how one could for example pick up randomly (or first) 20 brain samples from GTex and download all the corresponding bigwig files for them? (I wrote brain because it looks like it is how recount2 splits GTex into when looking here: https://jhubiostatistics.shinyapps.io/recount/ )

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This is a separate question, please post a new question Daniel. Thank you =)

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