How to make GFF file based on assembled transcriptome and genome sequence?

Question

[ahmad mousavi]

Hi

I have made an denovo transcriptome using Trinity and also the specie has the draft genome too.

For next projects ., We want to make GFF/GTF based on both assembled transcriptome and draft genome.

Actually, I need to know coordination of genes based on draft genome sequence position.

How can I map fasta transcriptome to draft genome in order to make GFF?

Or Is there any software to make GFF/GTF with using transcriptome and genome sequence?

thanks.

Answer 1

[h.mon]

You can map the assembled transcriptome to the draft genome, both SPALN and GMAP perform this task and output a GFF file.

However, transcriptome assemblies with short data are noisy (chimeric and truncated transcripts, transcripts split in two or more, contaminants and other artifacts), and the above mapping will not provide an accurate structure of the underlying gene for many transcripts. You would need to use some genome annotation pipeline (e.g. Maker or Bracker) to get a better structure of the gene models.

[ahmad mousavi]

great thanks, the problem is that my genome is also not complete too.the current pipeline cannot find the exact region such as TSS or Exon,.... Do you have any idea about softwares which could determine those regions?

tnx.

[colindaven]

Try gmap with gff3 output for this with the transcripts from your Trinity output.

It makes sense to quality check your genome using BUSCO if possible. Did you just use short reads for your assembly? If so it is likely to be very fragmented.

[ahmad mousavi]

Yes we done Maker before, but our genome is partial too, so at the moment we performed Trinity and we have to make GFF based on Genome file.

the gmap gff3 output is also good but I have no idea how to merged that with genome sequence to find exon, intron and TSS regions?