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.
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written
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ahmad mousavi
You are looking for Splice aware alignment tools or pipelines using them. Many exist:
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
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.
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?
Look at the Readme here https://github.com/lh3/minimap2 it should be sam format not paf.
So yes it is fine
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