how to integrate the blastx output into transcriptome assembly?

Question

[seta]

Hi all,

I did transcriptome assembly and blastx against some databases, like uniprot, NR, and refseq. Now, I would like to assign the blastx output to contigs, please let me know how I should integrate the blastx results on each contig within the assembly? Thanks in advance.

Answer 1

[GouthamAtla]

It may be not a direct answer to your question but, I would suggest to use Annocript. It annotates the transcripts and gives you a GFF file with all the annotated information. You can read more info here. Have a look at the output generated.

[seta]

Thanks friend. Actually, I'm in a doubt about using Annocript or Trinotate. If you have any experience with these two program, please let me know your idea about it, pros and cons? Thanks

Answer 2

[Antonio R. Franco]

Look information about the generation of gff or gtf files