Question: Gene predection or gene information extension from available gtf file.
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gravatar for bhagyathimmappa
2.4 years ago by
bhagyathimmappa10 wrote:

May be 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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by bhagyathimmappa10

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

ADD REPLYlink written 2.4 years ago by colindaven1.9k

Thank you, I will try and let you know.

ADD REPLYlink written 2.4 years ago by bhagyathimmappa10
0
gravatar for Hussain Ather
2.4 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

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.

ADD COMMENTlink written 2.4 years ago by Hussain Ather940
0
gravatar for bhagyathimmappa
2.4 years ago by
bhagyathimmappa10 wrote:

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

ADD COMMENTlink written 2.4 years ago by bhagyathimmappa10
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