Illumina HumanOmniExpress IDAT files
3
0
Entering edit mode
6.5 years ago

Hi, 

I've got some Illumina HumanOmniExpress Genotyping Chip IDAT files and I was wondering if there are any packages that people know of that can read them? Are the IDAT files for this chip encrypted to a point where I'd have to use genome studio?

Thanks, 

illumina idat • 4.7k views
ADD COMMENT
0
Entering edit mode

After a bit of digging, I found the cram package, which seems to do what I want - Any other suggestions are welcome! 

ADD REPLY
0
Entering edit mode

hallo, did you know how to read IDAT files in R? and how about the script? I tried to use "read.idat",but there always were error:

Error in `[.data.frame`(bgx$controls, , c("Probe_Id", "Array_Address_Id")) : 
  undefined columns selected

or

Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
  cannot open compressed file 'HumanHT-12_V4_0_R2_15002873_B_WGDASL.bgx', probable reason 'No such file or directory'

Looking forward to your reply. and many thanks!

ps: I cannot use Genome Studio software, that's why only R I can use.

ADD REPLY
1
Entering edit mode
3.5 years ago
freeseek ▴ 120

I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand.

ADD COMMENT
0
Entering edit mode
5.6 years ago
niutster ▴ 100

Hi,

There are several packages you can use them. Refer to "Review of processing and analysis methods for DNA methylation array data" paper. In this paper you can find them.

ADD COMMENT
0
Entering edit mode

That paper is in reference to Methylation data, not Genotyping data.

ADD REPLY
0
Entering edit mode
4.9 years ago
jmzeng1314 ▴ 130

The same question : how to analysis HumanOmni5 Exome-4v1-2 Array data ?

you can just use Genome Studio to analysis IDAT files, but you should figure out their original file names.

ADD COMMENT
0
Entering edit mode

Genome Studio is proprietary software, and not open source. I mention in the OP that I was looking for alternatives to Genome Studio.

ADD REPLY

Login before adding your answer.

Traffic: 1793 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