Question: Gene predection or gene information extension from available gtf file.
0
gravatar for bhagyathimmappa
19 months 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 19 months ago • written 19 months 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 19 months ago by colindaven1.2k

Thank you, I will try and let you know.

ADD REPLYlink written 19 months ago by bhagyathimmappa10
0
gravatar for Hussain Ather
19 months ago by
Hussain Ather910
National Institutes of Health, Bethesda, MD
Hussain Ather910 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 19 months ago by Hussain Ather910
0
gravatar for bhagyathimmappa
19 months ago by
bhagyathimmappa10 wrote:

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

ADD COMMENTlink written 19 months ago by bhagyathimmappa10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 523 users visited in the last hour