Question: Convert Blastx Results To Gtf
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gravatar for upendrakumar.devisetty
6.6 years ago by
United States
upendrakumar.devisetty350 wrote:

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.

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ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 6.6 years ago by upendrakumar.devisetty350
0
gravatar for Istvan Albert
6.6 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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/

ADD COMMENTlink written 6.6 years ago by Istvan Albert ♦♦ 79k

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.

ADD REPLYlink written 6.6 years ago by upendrakumar.devisetty350

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.

ADD REPLYlink written 6.6 years ago by Istvan Albert ♦♦ 79k

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

ADD REPLYlink written 9 months ago by lieven.sterck4.2k
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