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how to integrate the blastx output into transcriptome assembly?

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.

rna-seq sequencing blast alignment
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updated by Ram Ram • written by seta seta

2 answers

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.

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updated by Ram Ram • written by GouthamAtla GouthamAtla

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

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written by seta seta

Look information about the generation of gff or gtf files

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updated by Ram Ram • written by Antonio R. Franco Antonio R. Franco

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