Question

Crlmm HumanOmniExpress-24v1 Annotation not available

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andrew.j.skelton73 ▴ 370

@andrewjskelton73-7074

Last seen 8 months ago

United Kingdom

Hi,

I've got some Illumina HumanOmniExpress-24v1 data, and I was going to use Crlmm to read the IDAT files in and carry out genotyping, but the 24 well version of the chip doesn't seem to be available, I was wondering if there was going to be support for it?

Any suggestions for alternatives would be welcome!

Thanks,

crlmm • 1.8k views

ADD COMMENT • link updated 6.5 years ago by lack.justin • 0 • written 9.3 years ago by andrew.j.skelton73 ▴ 370

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I guess an alternative is to split the IDAT files into two sets of 12, as they're essentially the same chip, just 12/24 well versions. Anyone have any experience with this?

ADD REPLY • link 9.3 years ago andrew.j.skelton73 ▴ 370

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lack.justin • 0

@lackjustin-16172

Last seen 6.5 years ago

Has there ever been a solution to this problem? I have Infinium® CoreExome-24 v1.2 BeadChip data that I want to develop an automated workflow for, and there doesn't appear to be an annotation set for this chip. Are we able to provide our own annotation set? If so, are there specific files from the Illumina chip support files? Is there a format guide for the annotation?

Thank you in advance for your help.

Justin

ADD COMMENT • link 6.5 years ago lack.justin • 0

score 2 · Accepted Answer · 2015-08-07

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Matthew Ritchie ▴ 1000

@matthew-ritchie-650

Last seen 7 months ago

Australia

Hi Andrew,

We don't currently support this platform, but are working towards an approach to handle data from any arbitrary platform without the need for a chip-specific package - we hope to make it available in the next release. Best wishes,

Matt

ADD COMMENT • link 9.3 years ago Matthew Ritchie ▴ 1000

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Cheers Matt, any idea on the time scale for the next release?

ADD REPLY • link 9.3 years ago andrew.j.skelton73 ▴ 370