ChIPSeeker enrichPeakOverlap external dataset downloads
1
0
Entering edit mode
rbronste ▴ 60
@rbronste-12189
Last seen 23 months ago

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'

 

chipseeker chipseq chip • 1000 views
ADD COMMENT
0
Entering edit mode

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 REPLY
2
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

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 COMMENT
1
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

devtools::install_github('GuangchuangYu/ChIPseeker')

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 397 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6