Question: ChIPSeeker enrichPeakOverlap external dataset downloads
0
gravatar for rbronste
20 months ago by
rbronste60
rbronste60 wrote:

I am trying to import mm10 ChIP BED file datasets from GEO for use with: 

enrichPeakOverlap
downloadGEObedFiles(genome="mm10", destDir = getwd())

However I am getting the following errors, not sure what the issue is:

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1308nnn/GSM1308182/suppl/GSM1308182_HaloSox2D.bed.gz'
Content type 'unknown' length 103463 bytes (101 KB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1386nnn/GSM1386022/suppl/GSM1386022_4cell_mc_CG_raw.bedGraph.gz'
Error in download.file(fnames[i], destfile = destfiles[i], mode = "wb") : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1386nnn/GSM1386022/suppl/GSM1386022_4cell_mc_CG_raw.bedGraph.gz'
In addition: Warning message:
In download.file(fnames[i], destfile = destfiles[i], mode = "wb") :
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1386nnn/GSM1386022/suppl/GSM1386022_4cell_mc_CG_raw.bedGraph.gz': FTP status was '550 Requested action not taken; file unavailable'

 

chipseq chipseeker chip • 602 views
ADD COMMENTlink modified 20 months ago by Guangchuang Yu1.1k • written 20 months ago by rbronste60

So basically it downloads about 10 files and then quits on this one because I guess it can't locate it. Any way around this?

ADD REPLYlink written 20 months ago by rbronste60
Answer: ChIPSeeker enrichPeakOverlap external dataset downloads
2
gravatar for Guangchuang Yu
20 months ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

By visiting GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1386022, I find that the `raw.bedGraph.gz` file was removed and instead they provide `bed.gz` files.

1. I need to update GEO meta information.

2. Need to change `downloadGEObedFiles` to tackle with this situation, since I can guarantee the GEO meta info is always correct even it was updated frequently.

ADD COMMENTlink written 20 months ago by Guangchuang Yu1.1k
1
ADD REPLYlink written 20 months ago by Guangchuang Yu1.1k

Great thanks! Can I currently update this commit with update.packages("ChIPseeker")?

ADD REPLYlink written 20 months ago by rbronste60
1

devtools::install_github('GuangchuangYu/ChIPseeker')

ADD REPLYlink written 20 months ago by Guangchuang Yu1.1k

Is there any way to just retrieve the BED files and exclude the bedGraph files?

ADD REPLYlink written 20 months ago by rbronste60
1

try getGEOInfo('mm10') and process the data frame before downloading files.

ADD REPLYlink written 20 months ago by Guangchuang Yu1.1k
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