A question about converting gtf file to bed12 file

[Keren Zhou]

Dear UCSC Genome Team,

I'm a PhD student, and I want to convert the current version of mouse GENCODE annotation set vM5 to bed12 file. I know that there are two programs, named gtfTogenePred and genePredToBed, can complete this job. 

Here I have a question. We know that there is something difference between the old version and the newer version (e.g. human GENCODE v19 and human GENCODE v23).So, my question is do the two programs work well when dealing with different versions of GENCODE annotation sets?

Thank you! I hope for hearing from you!

Best wishes,

Zhoukr

[Luvina Guruvadoo]

Hello Zhoukr,

Thanks for your question. Yes, both gtfToGenePred and genePredToBed will work with different versions of GENCODE annotation sets.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

--