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svm-zhang / AGOUTI

Annotated Genome Optimization Using Transcriptome Information
https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0136-3
MIT License
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'gap' feature request #3

Closed TakashiKoyama closed 8 years ago

TakashiKoyama commented 8 years ago

Hi Simo,

I want to know which 'N's AGOUTI added after the scaffolding. Could you consider adding 'gap' features in the revised gff?

Takashi

svm-zhang commented 8 years ago

Hi Takashi,

So you'd like to know coordinates of gaps in the GFF, like the following?

scaf_1 AGOUTI gap 1000 2000 . . . ID=...;

Do I understand you here right?

Simo

TakashiKoyama commented 8 years ago

Hi Simo,

Yes. Is it possible?

Takashi

svm-zhang commented 8 years ago

Hi Takashi,

It's possible. Please give me some time for this. I have a deadline at hand and it might take a bit longer. I will let you know.

Simo

TakashiKoyama commented 8 years ago

Hi Simo,

OK. Thank your for your kind helps!

Takashi

svm-zhang commented 8 years ago

Hi Takashi,

I just made a new patch. Could you give a try? Now in the GFF, you will have scaffold and gap features, like:

scaf_1 AGOUTI scaffold 1 10000 . . . ID=scaf_1 scaf_1 AGOUTI gap 2000 3000 . . . Parent=scaf_1 ... gene models on scaf_1 ...

Note that the positions are 1-based. Hope this helps!

Please let me know if this works for you.

Simo

TakashiKoyama commented 8 years ago

Hi Simo,

Everything works great! Thank you for your quick work!

Takashi

svm-zhang commented 8 years ago

No problem Takashi! Glad to help!

I am gonna close this thread now.