Convert Blastx Results To Gtf

Question

[upendrakumar.devisetty]

Does anyone know how to convert blastx result to gtf. My main purpose of doing this is to convert my denovo transcriptome assembly fasta file into gtf (via blastx), so that i can use cuffcompare to compare the reference gff and denovo gtf and then only extract novel transcripts out of my denovo transcriptome. Does my work flow is feasible. Basically we don't want to annotate my denovo transcriptome assembly and only extract those transcripts that are novel from my denovo transcritpome assembly.

Answer 1

[Istvan Albert]

There is this discussion on converting blast to GFF, you would need to generate blast results in the column oriented format, then it is just a matter of rearranging the columns:

http://www.biostars.org/post/show/277/how-to-convert-blast-results-to-gff/

[upendrakumar.devisetty]

Thanks. I have noticed that as well. But my problem is converting GFF file produced using that script to GTF. It never worked for me.

[Istvan Albert]

GTF and GFF are very similar - the only differences are in the last column the attribute formatting, so that on its own is not a problem.

What is however a problem that I only realized right now is that you will need to fill in a lot of attributes in a very specific manner - the problem is far more complicated than a mere conversion of outputs you would need to find the right methodology that allows you to compute the isoform abundances from a blast results and fill that in exactly the way cuffdiff would because that is how cuffcompare expects it.

[lieven.sterck]

perhaps have a look at this post? : Convertion Of Gff3 To Gtf