Question: How to make annotation (GFF/GTF) for transcriptome?
gravatar for ahmad mousavi
10 weeks ago by
ahmad mousavi480
Royan Institute, Tehran, Iran
ahmad mousavi480 wrote:


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.

ADD COMMENTlink modified 10 weeks ago by Juke344.5k • written 10 weeks ago by ahmad mousavi480
gravatar for Juke34
10 weeks ago by
Juke344.5k wrote:

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,

ADD COMMENTlink modified 9 weeks ago • written 10 weeks ago by Juke344.5k
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