Gene loss in subsequent round of maker for fungal genome annotation

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Gene loss in subsequent round of maker for fungal genome annotation

Urmi

Hello maker community,

I am trying to run maker 3.01.02-beta on a fungal genome. I am using available EST and protein sequences from a different strain of the same species using parameters "est" 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: 12796 total genes out of which 12771 have AED < 0.5
  • run B:10713 total genes out of which 10701 have AED < 0.5
  • run C: 12651 total genes out of which 12582 have AED < 0.5
Looking at the gff files in detail, it is observerd that there are some gene models in run A which are lost in run B and gain in run C. I don't understand why there is gene loss for run B. Here is an example:

RunA

contig1 maker   gene    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34
contig1 maker   mRNA    20468   21193   100     +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|0|1|0|241
contig1 maker   exon    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:cds;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 blastn  expressed_sequence_match        20468   21193   726     +       .       ID=contig1:hit:983:3.2.0.0;Name=jgi|test_1|140804|est target_length=726
contig1 blastn  match_part      20468   21193   726     +       .       ID=contig1:hsp:998:3.2.0.0;Parent=contig1:hit:983:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
contig1 est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1022:3.2.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100
contig1 est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1110:3.2.0.0;Parent=contig1:hit:1022:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunB:
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunC: 
contig1 maker   gene    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5
contig1 maker   mRNA    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1;Parent=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|241;_merge_warning=1
contig1 maker   exon    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:1;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:cds;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 snap_masked     match   20468   21193   42.956  +       .       ID=contig1:hit:5240:4.5.0.0;Name=snap_masked-contig1-abinit-gene-0.5-mRNA-1;target_length=4075195
contig1 snap_masked     match_part      20468   21193   42.956  +       .       ID=contig1:hsp:12911:4.5.0.0;Parent=contig1:hit:5240:4.5.0.0;Target=snap_masked-contig1-abinit-gene-0.5-mRNA-1 1 726 +;Gap=M726
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

Please could anyone shed come light on this?


Many thanks in advance.

Urmi


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Re: Gene loss in subsequent round of maker for fungal genome annotation

Urmi
Further to this, I did run interproscan on all three runs and 100% of the genes from all of them have protein domains found. I am confused which one should I consider as the best annotation. I am sorry for so many questions but I am very new to maker. 

Thanks again for any help you could provide. 

On Wed, Mar 21, 2018 at 9:05 AM, Urmi <[hidden email]> wrote:

Hello maker community,

I am trying to run maker 3.01.02-beta on a fungal genome. I am using available EST and protein sequences from a different strain of the same species using parameters "est" 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: 12796 total genes out of which 12771 have AED < 0.5
  • run B:10713 total genes out of which 10701 have AED < 0.5
  • run C: 12651 total genes out of which 12582 have AED < 0.5
Looking at the gff files in detail, it is observerd that there are some gene models in run A which are lost in run B and gain in run C. I don't understand why there is gene loss for run B. Here is an example:

RunA

contig1 maker   gene    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34
contig1 maker   mRNA    20468   21193   100     +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|0|1|0|241
contig1 maker   exon    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:cds;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 blastn  expressed_sequence_match        20468   21193   726     +       .       ID=contig1:hit:983:3.2.0.0;Name=jgi|test_1|140804|est target_length=726
contig1 blastn  match_part      20468   21193   726     +       .       ID=contig1:hsp:998:3.2.0.0;Parent=contig1:hit:983:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
contig1 est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1022:3.2.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100
contig1 est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1110:3.2.0.0;Parent=contig1:hit:1022:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunB:
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunC: 
contig1 maker   gene    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5
contig1 maker   mRNA    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1;Parent=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|241;_merge_warning=1
contig1 maker   exon    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:1;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:cds;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 snap_masked     match   20468   21193   42.956  +       .       ID=contig1:hit:5240:4.5.0.0;Name=snap_masked-contig1-abinit-gene-0.5-mRNA-1;target_length=4075195
contig1 snap_masked     match_part      20468   21193   42.956  +       .       ID=contig1:hsp:12911:4.5.0.0;Parent=contig1:hit:5240:4.5.0.0;Target=snap_masked-contig1-abinit-gene-0.5-mRNA-1 1 726 +;Gap=M726
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

Please could anyone shed come light on this?


Many thanks in advance.

Urmi




--
"The only way of finding the limits of the possible is by going beyond them into the impossible." - Arthur C. Clarke

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Re: Gene loss in subsequent round of maker for fungal genome annotation

Carson Holt-2
In reply to this post by Urmi
Run A —> no gene prediction, just cut and paste of transcript/protein alignments to generate rough models.
Run B —> Gene predictions based on training using only highly conserved subset of genes (you will have low sensitivity)
Run C —> Gene predictions based on training using broader gene set. Higher sensitivity but potentially lower specificity (sensitivity gains should outweigh any specificity loss).

Finally, mnake sure you look at models in a browser to see how well evidence and models overlap. If gene fusion is an issue (falsely merged mRNA-seq assembly results will generate hints that can cause gene predictors to fuse gene models), try deFusion —> https://wjidea.github.io/defusion/installation.html

—Carson



On Mar 21, 2018, at 3:05 AM, Urmi <[hidden email]> wrote:

Hello maker community,

I am trying to run maker 3.01.02-beta on a fungal genome. I am using available EST and protein sequences from a different strain of the same species using parameters "est" 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: 12796 total genes out of which 12771 have AED < 0.5
  • run B:10713 total genes out of which 10701 have AED < 0.5
  • run C: 12651 total genes out of which 12582 have AED < 0.5
Looking at the gff files in detail, it is observerd that there are some gene models in run A which are lost in run B and gain in run C. I don't understand why there is gene loss for run B. Here is an example:

RunA

contig1 maker   gene    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34
contig1 maker   mRNA    20468   21193   100     +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|0|1|0|241
contig1 maker   exon    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:cds;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 blastn  expressed_sequence_match        20468   21193   726     +       .       ID=contig1:hit:983:3.2.0.0;Name=jgi|test_1|140804|est target_length=726
contig1 blastn  match_part      20468   21193   726     +       .       ID=contig1:hsp:998:3.2.0.0;Parent=contig1:hit:983:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
contig1 est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1022:3.2.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100
contig1 est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1110:3.2.0.0;Parent=contig1:hit:1022:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunB:
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunC: 
contig1 maker   gene    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5
contig1 maker   mRNA    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1;Parent=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|241;_merge_warning=1
contig1 maker   exon    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:1;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:cds;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 snap_masked     match   20468   21193   42.956  +       .       ID=contig1:hit:5240:4.5.0.0;Name=snap_masked-contig1-abinit-gene-0.5-mRNA-1;target_length=4075195
contig1 snap_masked     match_part      20468   21193   42.956  +       .       ID=contig1:hsp:12911:4.5.0.0;Parent=contig1:hit:5240:4.5.0.0;Target=snap_masked-contig1-abinit-gene-0.5-mRNA-1 1 726 +;Gap=M726
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

Please could anyone shed come light on this?


Many thanks in advance.

Urmi

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[hidden email]
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Re: Gene loss in subsequent round of maker for fungal genome annotation

Urmi
That's great! Thanks for the tips Carson. 

Urmi

On Fri, Mar 23, 2018 at 5:28 PM, Carson Holt <[hidden email]> wrote:
Run A —> no gene prediction, just cut and paste of transcript/protein alignments to generate rough models.
Run B —> Gene predictions based on training using only highly conserved subset of genes (you will have low sensitivity)
Run C —> Gene predictions based on training using broader gene set. Higher sensitivity but potentially lower specificity (sensitivity gains should outweigh any specificity loss).

Finally, mnake sure you look at models in a browser to see how well evidence and models overlap. If gene fusion is an issue (falsely merged mRNA-seq assembly results will generate hints that can cause gene predictors to fuse gene models), try deFusion —> https://wjidea.github.io/defusion/installation.html

—Carson



On Mar 21, 2018, at 3:05 AM, Urmi <[hidden email]> wrote:

Hello maker community,

I am trying to run maker 3.01.02-beta on a fungal genome. I am using available EST and protein sequences from a different strain of the same species using parameters "est" 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: 12796 total genes out of which 12771 have AED < 0.5
  • run B:10713 total genes out of which 10701 have AED < 0.5
  • run C: 12651 total genes out of which 12582 have AED < 0.5
Looking at the gff files in detail, it is observerd that there are some gene models in run A which are lost in run B and gain in run C. I don't understand why there is gene loss for run B. Here is an example:

RunA

contig1 maker   gene    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34
contig1 maker   mRNA    20468   21193   100     +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|0|1|0|241
contig1 maker   exon    20468   21193   .       +       .       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:cds;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
contig1 blastn  expressed_sequence_match        20468   21193   726     +       .       ID=contig1:hit:983:3.2.0.0;Name=jgi|test_1|140804|est target_length=726
contig1 blastn  match_part      20468   21193   726     +       .       ID=contig1:hsp:998:3.2.0.0;Parent=contig1:hit:983:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726
contig1 est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1022:3.2.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100
contig1 est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1110:3.2.0.0;Parent=contig1:hit:1022:3.2.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunB:
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

RunC: 
contig1 maker   gene    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5
contig1 maker   mRNA    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1;Parent=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|241;_merge_warning=1
contig1 maker   exon    20468   21193   .       +       .       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:1;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 maker   CDS     20468   21193   .       +       0       ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:cds;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
contig1 snap_masked     match   20468   21193   42.956  +       .       ID=contig1:hit:5240:4.5.0.0;Name=snap_masked-contig1-abinit-gene-0.5-mRNA-1;target_length=4075195
contig1 snap_masked     match_part      20468   21193   42.956  +       .       ID=contig1:hsp:12911:4.5.0.0;Parent=contig1:hit:5240:4.5.0.0;Target=snap_masked-contig1-abinit-gene-0.5-mRNA-1 1 726 +;Gap=M726
contig1 est_gff:est2genome      expressed_sequence_match        20468   21193   3630    +       .       ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
contig1 est_gff:est2genome      match_part      20468   21193   3630    +       .       ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est 1 726 +;Gap=M726

Please could anyone shed come light on this?


Many thanks in advance.

Urmi

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