How to change scaffold.fasta file or scaffold.bed file to GTF file?

Question

[worarado.kan]

Hello everyone,

I have a problem about changing scaffold.fasta file or scaffold.bed file to GTF file. I would like to analyse using HISAT,stringtie and ballgown that required GTF file of reference. I try to do follow these website but still not complete.

How To Convert Bed Format To Gtf?

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

https://github.com/pfurio/bed2gtf

Please give me the guidance.

Thank you

[WouterDeCoster]

I try to do follow these website but still not complete.

Please be as specific as possible. What do you get and how does that not correspond with what you want?

Which organism are you working on?

[Bastien Hervé]

You can not go from a fasta file to gtf file.

What do you have as bed file ? If you only have chr/start/end informations you will not be able to convert your bed to gtf. Informations like transcript_id and many others will be missing.

If you have a bed file comming from a gtf file you will be able to do the reverse change with gtf2bed as explained in your link (How To Convert Bed Format To Gtf?)

Answer 1

[alejandrogzi]

Hi, if you need to convert a .bed file to a .gtf file to use it as input to HISAT2, you must likely need bed2gtf