Entering edit mode
6.9 years ago
haiying.kong
▴
360
I would like to find out how many genes are in the targeted area for a given Agilent protocol for WES. Agilent website gives only the number of probes, and among the dataset I downloaded, there is one txt file, like: S07604624_Targets.txt gives a list of names. But the list of names is mixture of gene symbol, Ensembl Transcript ID, GenBank ID, Refseq ID, and about 22% of them are not having corresponding gene symbols if I use the database: org.Hs.eg.db.
[1] "KJ891129" "X98054" "ENST00000369829" "NM_173803"
[5] "BC172493" "ENST00000371910" "ENST00000491059" "NM_001301039"
[9] "CCDS60146.1" "ENST00000559981" "AK098124" "CU688405"
[13] "ENST00000511269" "ENST00000522231" "ENST00000449052" "KJ895283"
[17] "AK075206" "CCDS4839.1" "ENST00000396353" "AB463204"
[21] "AF338924" "AK124803" "KJ902737" "CCDS46147.1"
[25] "L38251" "AK097145" "CCDS47799.1" "NM_032125"
[29] "ENST00000409413" "AK294470" "AB749845" "U93181"
[33] "ENST00000502829" "CU689180" "ENST00000329451" "AK024678"
[37] "CCDS7428.1" "ENST00000515224" "AK296850" "ENST00000458599"
[41] "AB464008" "Z15108" "AK314242" "BC022387"
[45] "ENST00000531291" "ENST00000374450" "BX647401" "ENST00000477633"
[49] "KJ903845" "ENST00000529099" "NM_014423" "CCDS2110.1"
[53] "CCDS13496.1" "NR_026580" "CCDS46257.1" "NM_207355"
I thought this is a basic information Agilent would provide. Where can I find this information, or how can I calculate this?
Maybe you can ask an Agilent sales person? They always seem to know everything.
I don't know about that... They keep on calling me if I want to use their kit. Apparently, they don't know yet how to f*ck off.