How to convert a .gtf file to hints file?

Question

[Mehmet]

Hi,

I want to convert a gtf file to hints file. For this, what should I do?

[Manvendra Singh]

what is hints file ?

can you please describe it ?

[Mehmet]

Hi,

I have a .gtf file which will be used on augustus gene prediction, but I think I have to convert it to hints file.

[Alex Reynolds]

What is a hints file?

[Mehmet]

I will probably use CDS type of hints.

[Mehmet]

I have prepared a .gtf file which contains only intron part. How can I convert this file to a type of hints file (intron part). There are 16 types of hints file which are start, stop, tss, tts, ass, dss, exonpart, exon, intronpart, intron, CDSpart, CDS, UTRpart, UTR, impart, nonexonpart.

[Devon Ryan]

It should be apparent that no one has any clue what a "hints" file is. Without knowing that, we can't help you. You need to post a link to a webpage or a paper describing this "hints" file format.

[Mehmet]

http://augustus.gobics.de/binaries/README.TXT

Hi. At this link, you could see at steps 5.

[Mehmet]

Thank you very much. I am actually at a beginner level at Bioinformatics, so I generally get difficulties. Your helps are so grateful.

Answer 1

[Devon Ryan]

According to the link you posted, a "hints" file is a GFF/GTF file with a source= field in the last column. The sources are specified in a configuration file that's also described at the link you posted.