Gene predection or gene information extension from available gtf file.

Question

[bhagyathimmappa]

May be a dumb question

Hello all,

for a given fungi there is assembly with 99contig and gtf file available, we have sequenced sensitive strain and did denovo assembly. For further work I need to generate gtf file for denovo assembly (sensitive strain for which we need to map gene location).

I am not sure how to do it, do I need to do abinitio gene prediction? or is there any way I can use the existing gtf file and modify it?

I am new to this filed, I am sorry if i am asking something which does not make sense.

Oh ya, sensitive reads show 98.8% alignment rate to existing assembly.

Thanks in advance

Bhagya C T

[colindaven]

I would do this:

• install maker - quite difficult - or use it on cyverse
• extract transcript sequences or ORF seqs from existing GTF, eg with transdecoder or similar
• map to contigs with gmap
• There you have a decent GFF3 file.

There is a fungi specific genefinder, I think it s called snowyowl or similar. Also Augustus is quite good

[bhagyathimmappa]

Thank you, I will try and let you know.

Answer 1

[Hussain Ather]

What kind of file do you have? Fasta?

If so, there's a tuxedo suite protocol (for RNA-Seq, Chip-Seq, etc.) to follow. You align the sequences against a reference genome and generate bed files which are processed. Those bed files are converted to gtf.

Answer 2

[bhagyathimmappa]

I have .fasta file which is my denovo assembly file.