Exon Coordinates Of Hg19 Genome related question.. for ExomDepth(CNV analysis)

Question

[younhee.ko]

I would like to know the exact exon postion for gene based on hg19.

I have downloaded the refFlat file from the following site. (gene model based on hg19) http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

refFlat file include the all the possible gene isoform as well as exon postion.

However, these coordinates would not match with the exon positions in ExomDepth package for CNV analysis.... (even though it is relatively new version . note that "http://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf"

ExomeDepth manual said that

> library(ExomeDepth)

>exons.hg19[100:200,]

179          1 1216042 1216046    SCNN1D_1
180          1 1216606 1216677    SCNN1D_2
181          1 1216791 1216990    SCNN1D_3
182          1 1217622 1217695    SCNN1D_4
183          1 1219358 1219470    SCNN1D_5
184          1 1220951 1221044    SCNN1D_6
185          1 1221306 1221658    SCNN1D_7
186          1 1222148 1222355    SCNN1D_8
187          1 1222489 1222679    SCNN1D_9
188          1 1222888 1222976   SCNN1D_10
189          1 1223053 1223216   SCNN1D_11
190          1 1223319 1223417   SCNN1D_12
191          1 1225651 1225768   SCNN1D_13
192          1 1225857 1225935   SCNN1D_14
193          1 1226017 1226074   SCNN1D_15
194          1 1226275 1226333   SCNN1D_16
195          1 1226445 1226520   SCNN1D_17
196          1 1226634 1226990   SCNN1D_18

but if I find the gene SCNN1D exon postion from refFlat file I download from UCSC(http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/)

   Exon postions from refFlat file
exon1_start, exon1_end, exon2_start, exon2_end......  1215815,1216605,1216790,1217621,1219357,1221305,1222147,1222488,1222887,1223052,1223318,1225650,1225856,1226016,1226274,1226444,1226633,        1216046,1216677,1216990,1217695,1219470,1221658,1222355,1222679,1222976,1223216,1223417,1225768,1225935,1226074,1226333,1226520,1227409,

It is really different. even though the number of exon is also different.. refFlat say.. 17 but ExomDepth Package say.. 18.. . What I have to trust?? ExomDepth R package is wrong ?? or Do I miss something?

[Devon Ryan]

Since exomeDepth appears to be using the Ensembl annotation, have you compared the coordinates versus that? Ensembl and UCSC won't always agree (Ensembl is usually better, in my opinion).

[younhee.ko]

Thanks Devon

As you mentioned, I also checked with Ensembl Exon information. However, it looks different with others too. ;( So frustrating

Here is the one I downloaded from BIOmart.

What I have to do it? Any suggestion??

Answer 1

[Joakim]

The built in exon annotation exon #2: 180 1 1216606 1216677 SCNN1D_2

...seems to match exon #2 in ENSEMBL: ENSG00000162572,ENST00000379116,1,1215816,1227409,1,SCNN1D,8,1216606,1216677,ENSE00003396173

...and ucsc exon#1 ends at 1216605

I would think, since it is designed for exomes, there's is a change in the UTR annotation (usually exon #1 only) in the build in version.

You can use your own exon annotation instead of the build in. Since our lab is changing to hg38, instead of using bedframes from data(genes.hg19) and data(exons.hg19) in ExomeDepth, I got them from the UCSC Table Browser for hg38 (http://genome.ucsc.edu/cgi-bin/hgTables). They only contains the following info: chromosome start end name. I renamed the columns similarly to exons.hg19 just in case: colnames(exons.hg38) <- c("chromosome", "start", "end", "name").