pred_gff problem

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pred_gff problem

Eric Ross
I'm using a gff file, created with the included cufflinks2gff3 script as a pred_gff in my maker run.  The maker run seems to have collapsed all of the input gff match_part lines.  Do I have a formatting problem with my input? 

The maker that results from this prediction has the same problem and so I lean toward it being and input/processing error rather than just an output issue.

input gff excerpt:

v31.023451      Cufflinks       match   8881    9977    17.893639       +      ID=4:CUFF.255943.0;Name=4:CUFF.255943.0;
v31.023451      Cufflinks       match_part      8881    9438    17.893639      ID=4:CUFF.255943.0:exon-1;Name=4:CUFF.255943.0;Parent=4:CUFF.255943.0;Target=4:CUFF.255943.0 1 558 +;
v31.023451      Cufflinks       match_part      9518    9803    17.893639      ID=4:CUFF.255943.0:exon-2;Name=4:CUFF.255943.0;Parent=4:CUFF.255943.0;Target=4:CUFF.255943.0 559 844 +;
v31.023451      Cufflinks       match_part      9863    9977    17.893639      ID=4:CUFF.255943.0:exon-3;Name=4:CUFF.255943.0;Parent=4:CUFF.255943.0;Target=4:CUFF.255943.0 845 959 +;

output gff excerpt:

v31.023451      pred_gff:cufflinks      match   8881    9977    1000    +      ID=v31.023451:hit:86965;Name=pred_gff_cufflinks-v31.023451-abinit-gene-0.8-mRNA-1;_AED=0.14;score=1000;
v31.023451      pred_gff:cufflinks      match_part      8881    9977    1000   ID=v31.023451:hsp:174762;Parent=v31.023451:hit:86965;Name=pred_gff_cufflinks-v31.023451-abinit-gene-0.8-mRNA-1;Target=pred_gff_cufflinks-v31.023451-abinit-gene-0.8-mRNA-1 1 1097 +;Gap=M1097;


Eric

--
Eric Ross
Alejandro Sánchez Alvarado Laboratory
Howard Hughes Medical Institute
Department of Neurobiology and Anatomy
University of Utah

http://planaria.neuro.utah.edu
[hidden email]


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Re: pred_gff problem

Carson Hinton Holt
Re: [maker-devel] pred_gff problem You would need to send me the input files for me to test.  Also you may want to come by the lab, we’ve done some very interesting analysis on the lamprey genome using mRNAseq to improve MAKER’s annotations.  You would be impressed by the results.  We could also talk about some more strategies to use on S. med. especially with the newly assembled transcriptome data presented at Cold Spring Harbor becoming available hopefully soon.

Carson



On 5/26/10 1:22 PM, "Eric Ross" <ejr@...> wrote:

I'm using a gff file, created with the included cufflinks2gff3 script as a pred_gff in my maker run.  The maker run seems to have collapsed all of the input gff match_part lines.  Do I have a formatting problem with my input? 

The maker that results from this prediction has the same problem and so I lean toward it being and input/processing error rather than just an output issue.

input gff excerpt:

v31.023451      Cufflinks       match   8881    9977    17.893639       +      ID=4:CUFF.255943.0;Name=4:CUFF.255943.0;
v31.023451      Cufflinks       match_part      8881    9438    17.893639      ID=4:CUFF.255943.0:exon-1;Name=4:CUFF.255943.0;Parent=4:CUFF.255943.0;Target=4:CUFF.255943.0 1 558 +;
v31.023451      Cufflinks       match_part      9518    9803    17.893639      ID=4:CUFF.255943.0:exon-2;Name=4:CUFF.255943.0;Parent=4:CUFF.255943.0;Target=4:CUFF.255943.0 559 844 +;
v31.023451      Cufflinks       match_part      9863    9977    17.893639      ID=4:CUFF.255943.0:exon-3;Name=4:CUFF.255943.0;Parent=4:CUFF.255943.0;Target=4:CUFF.255943.0 845 959 +;

output gff excerpt:

v31.023451      pred_gff:cufflinks      match   8881    9977    1000    +      ID=v31.023451:hit:86965;Name=pred_gff_cufflinks-v31.023451-abinit-gene-0.8-mRNA-1;_AED=0.14;score=1000;
v31.023451      pred_gff:cufflinks      match_part      8881    9977    1000   ID=v31.023451:hsp:174762;Parent=v31.023451:hit:86965;Name=pred_gff_cufflinks-v31.023451-abinit-gene-0.8-mRNA-1;Target=pred_gff_cufflinks-v31.023451-abinit-gene-0.8-mRNA-1 1 1097 +;Gap=M1097;


Eric

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