GtfToGenePred errors in converting GTF files.
0
1
Entering edit mode
9.3 years ago
tszn1984 ▴ 100

I want to convert the gtf file (gencode gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz) to genepred format. However, by using the UCSC gtfToGenepred executable, I had errors like this:

gunzip -c gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz |gtfToGenePred stdin test2.gpd
no exons defined for group ENSG00000223972.4, feature gene (perhaps try -ignoreGroupsWithoutExons)

I tried -ignoreGroupsWithoutExons. It worked but missed genes like -ignoreGroupsWithoutExons. Is there any general solution for this?

Thanks

software-error • 6.0k views
ADD COMMENT
0
Entering edit mode

Were you ever able to find a solution for this issue?

ADD REPLY

Login before adding your answer.

Traffic: 1595 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