Question: Gene loss in subsequent round of maker for fungal genome annotation
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gravatar for urmi208
13 months ago by
urmi20830
urmi20830 wrote:

Hello,

I am trying to run maker2.31.9 on a fungal genome. I have got transcript and protein sequences from a related species using parameters "altest" and "protein" in the maker_opts.ctl file. Here is the protocol I am using:

  1. Run maker with repeat masking and providing transcript and protein sequences from related species (Run A)
  2. Create SNAP model with CEGMA
  3. Train Augustus with BUSCO
  4. Run (run B ) with the new SNAP (done at step 2) and augustus species with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (altest_gff=runA_cdna2genome.gff, protein_gff=runA_protein2genome.gff3)
  5. Create SNAP model from run B.
  6. Train Augustus with transcripts from run B and BUSCO
  7. Run (run C ) with the new SNAP (done at step 5) and augustus species with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (altest_gff=runA_cdna2genome.gff, protein_gff=runA_protein2genome.gff3), keep_preds=1

As a result of this, I get following gene numbers:

  • run A: 12532 total genes out of which 12490 have AED < 0.5
  • run B:10038 total genes out of which 9996 have AED < 0.5
  • run C: 12909 total genes out of which 12133 have AED < 0.5

I don't understand why there is gene loss for run B. Please could anyone shed come light on this?

Many thanks in advance.

ADD COMMENTlink modified 13 months ago • written 13 months ago by urmi20830
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