Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

problem with transcript to genomic coordinates conversion when UTR spans more than 1 exon #44

Open
XiaoJianfeng opened this issue Aug 1, 2020 · 0 comments

Comments

@XiaoJianfeng
Copy link

transvar canno --refseq -i 'NM_000051.3:c.-30' --refversion hg19
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
NM_000051.3:c.-30 NM_000051.3 (protein_coding) ATM + chr11:g.108098322A/c.1-30A/. inside_[5-UTR;noncoding_exon_2] C2=NextToSpliceAcceptorOfExon2_At_chr11:108098321;dbxref=GeneID:472,HGNC:795,MIM:607585;aliases=NP_000042;source=RefSeq
transvar canno --refseq -i 'NM_000051.3:c.-31' --refversion hg19
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
NM_000051.3:c.-31 NM_000051.3 (protein_coding) ATM + chr11:g.108098321G/c.1-31G/. inside_[5-UTR;intron_between_exon_1_and_2] C2=SpliceAcceptorOfExon2_At_chr11:108098321;dbxref=GeneID:472,HGNC:795,MIM:607585;aliases=NP_000042;source=RefSeq

The position transvar gets for c.-31 is chr11:g.108098321. In fact, there is a large intron between c.-30 (the left most base of the exon 2) and c.-31 (the right most base of exon 1), and they are not next to each other. It seems transvar assumes UTR is always on the 1st exon.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant