I was wondering how many base pairs there are in All exon V4+UTR from Agilent manufacture.
Any thing that would help me understand the issue was appreciated.
The bed file of target regions can be downloaded from the earray site (need to register)
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Find Designs > SureSelect DNA > Agilent catalogue and download the S03723424 design files.
But the exon coordinate data of gtf downloaded from ucsc could not match that number. The related reference data were all from UCSC. I also wanted to use exon gtf there. Could you help explain that ? Thanks!
Agilent targets protein coding exons (CCDS and ENST genes), a selection of miRNAs, some of the NCBI genes etc... Not all UCSC genes will be on the Agilent V4 UTR, and some targets of the Agilent kit will not be on UCSC.
The full list of targets on the Agilent V4 UTR can be downloaded from the link at earray. The current version of Agilent is V6, which will have a different total target region.
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