Gene annotation help
1
0
Entering edit mode
6.2 years ago
mms140130 ▴ 60

I have downloaded gene annotation not sure from which website and I have the following data

geneName chrom txStart txEnd
A1BG    chr19       58858171 58864865
A1BG-AS1 chr19      58863335 58866549
A1CF chr10              52559168 52645435

then I looked at the UCSC website hg18 refFlat data and got the following

A1BG      chr19     63549983    63556677
A1BG-AS1    chr19   63555147    63558361
A1CF    chr10       52229174    52315441

which one to trust I have the same gene with same chromosome but different txstart and txend

Please help

Thanks

gene • 1.6k views
ADD COMMENT
3
Entering edit mode
6.2 years ago
Sparrow_kop ▴ 260

Hi, they are different version of genome assembly´╝î the former is hg19 or Grch37, the latter one is hg18, so different version has different coordinate. I suggest you use hg19 or hg38, which is better than hg18, you can download from UCSC Genome or Ensembl.

ADD COMMENT
0
Entering edit mode

Thank you very much that really helped :)

ADD REPLY

Login before adding your answer.

Traffic: 1756 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6