How to make annotation (GFF/GTF) for transcriptome?

Question

[ahmad mousavi]

Hi

I have a de novo transcriptome file and partial genome file which I need to make a (GFF/GTF) annotation map based on both transcriptome and draft genome information.

I have includes both scaffolds from Trinity and StringTie in order to make a comprehensive transcriptome. Nqow I need to make annotation based on both draft partial genome file and assembled transcriptome.

1- I have tried Pasa which mostly used GMAP, but is there any other pipeline for such purpose?

2- How can perform this process by myself with just applying softwares not pipelines?

Thanks for consideration and help.

Answer 1

[Juke34]

You are looking for Splice aware alignment tools or pipelines using them. Many exist:

• GMAP
• exonerate
• genomethreader
• spaln
• minimap2
• etc

Minimap2 is the fastest but you need to then convert the output to gff. You can do it with a script from AGAT, agat_convert_minimap2gff.pl

[Asan Emirsale]

I am looking for such workflow too. Great job, Jacques. But I didn't find a script named agat_convert_minimap2gff.pl in a Github repository of AGAT.

[Juke34]

Right I had modified the name to be more precise because minimap2 can output different formats. So it is agat_convert_minimap2_bam2gff.pl

[Asan Emirsale]

Thank you. But the way I first searched in that directory. Now it is clear for me. Thank you again. As I understood, the right minimap2 parametres for correct sam file output for agat_convert_minimap2_bam2gff.pl are minimap2 -ax splice:hq -uf, aren't it?

[Juke34]

Look at the Readme here https://github.com/lh3/minimap2 it should be sam format not paf. So yes it is fine