How to convert original BED file to a GTF ?

Question

[worarado.kan]

Hello everyone,

Now, I use Linux base for analyse HISAT2, Stringtie, ballgown. I have the original BED file and I would like to convert to GTF file for Stringtie analysis. If you have some suggestion about tool Or command for convert it, please let me know.

Thank you for your support Kan

[h.mon]

How To Convert Bed Format To Gtf?

http://onetipperday.sterding.com/2012/08/convert-bed-to-gtf.html

https://github.com/pfurio/bed2gtf

[worarado.kan]

Hi, I try to follow that website for change Bed file to gtf but can not. Do you have another kind suggestion?

Best,

[h.mon]

Which software and how was the command yo tried? What were the errors?

[worarado.kan]

I try to use this web https://github.com/pfurio/bed2gtf

Because another web I don't understand well. Could you explain again?

Thank you

[worarado.kan]

Thank you so much for your information.

Answer 1

[alejandrogzi]

Hi, here is one option that produces a complete-featured GTF ready to use in those tools: bed2gtf