#3 GTF to BED conversion link broken

[Phil Ewels]

Hi there,

In your documentation, you link to a Perl script which can be used to convert GTF files to BED format for use with RSeQC. Unfortunatlely, this link now seems to be broken - the code is now hosted on GitHub, here: https://github.com/ExpressionAnalysis/ea-utils/blob/master/clipper/gtf2bed

I really like many of the RSeQC tools and use them heavily, though I must admit the BED requirement is kind of annoying. Any chance of incorporating support for GTF inputs at some point?

Phil

[Liguo Wang]

Hi Phil,
broken link has been fixed.
We have no plan to support GTF as input. Most commonly used model organisms already have BED foramt annotation files avaialble from UCSC.

Thanks

-Liguo

[Phil Ewels]

Great stuff, thanks for the quick response! We work with a lot of non-model organisms I guess :) No problem though, I've now implemented the bed conversion step into our RNA analysis pipeline.

Phil