"uORF_starts_ends_GRCh37_PUBLIC.txt" strand information appears incorrect for some genes

[cbohrson]

ANKRD34A
ANXA8
CSAG1
GPR89A
MAGEA1
MAGEA12
NBPF15
NBPF9
NCOA4
NIPA2
PIAS3
POLR3C
POLR3GL
RNF115
TXNIP
ZNF488

E.g., for ANKRD34A the orientation is clearly forward, see below

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A145470496%2D145470981&hgsid=968486863_8b4bjUSE3ES524YFSyYRO6XAbnR9

Am I interpreting the meaning of 'strand' correctly? This is not a particularly serious issue but it is very odd for a tiny part of the file to be wrong and I wanted to report to make sure it wasn't a sign of some larger problem.

[XiaoleiZ]

Hi @cbohrson, the strand info is provided directly by Ensembl annotation instead of the plugin. If you think the strand info is problematic, I think the best way to solve it systematically is to raise that to VEP team https://github.com/Ensembl/ensembl-vep.

[cbohrson]

Thanks for the quick reply. I just wanted to make sure you understand what I originally posted.

In your GRCh37 uORF annotation, you have this line:

chr1 145470556 ANKRD34A reverse five_prime_utr 145470609

On the Ensembl browser, ANKRD34A is annotated as forward strand. Note there is a difference between GRCh37 and GRCh38 here - the gene is reverse, consistent with your annotation, on GRCh38.

While it's possible there is an issue in how VEP is using Ensembl annotations, given VEP is much more widely used than UTRannotator it seems more likely that the issue is how VEP is used here.

[XiaoleiZ]

I understand the issue is that the strand info for some genes has been updated in GRCh38 compared to GRCh37. In this case, the users shall switch to GRCh38 when using VEP. I agree this is a choice about how to use the VEP annotation. Then given the right strand info, our plugin can output the right 5'UTR specific annotation further.