Question: how to download bigwig from recount2?
0
gravatar for hyp15
3 months ago by
hyp150
hyp150 wrote:

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?

downloadstudy("SRP012682", type = "rse-gene") load(file.path("SRP012682", "rsegene.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 • 77 views
ADD COMMENTlink modified 3 months ago by Leonardo Collado Torres710 • written 3 months ago by hyp150
Answer: how to download bigwig from recount2?
1
gravatar for Leonardo Collado Torres
3 months ago by
United States
Leonardo Collado Torres710 wrote:

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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ADD COMMENTlink written 3 months ago by Leonardo Collado Torres710
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[1] D:/Documents/R/win-library/3.6
[2] D:/R/R-3.6.1/library
ADD REPLYlink written 3 months ago by Leonardo Collado Torres710
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


ADD REPLYlink written 3 months ago by Leonardo Collado Torres710

Thank you very much Leonardo Collado Torres!

ADD REPLYlink written 3 months ago by hyp150
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