convert transdecoder gff3 in to simple gff structure for genemarkET
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7.2 years ago
amoltej ▴ 90

HI I have trasndecoder generated gff3 file which looks like this -

asmbl_1 .       gene    1       1180    .       -       .       ID=asmbl_1|g.6;Name=ORF%20asmbl_1%7Cg.6%20asmbl_1%7Cm.6%20type%3A3prime_partial%20len%3A35%20%28-%29
asmbl_1 .       mRNA    1       1180    .       -       .       ID=asmbl_1|m.6;Parent=asmbl_1|g.6;Name=ORF%20asmbl_1%7Cg.6%20asmbl_1%7Cm.6%20type%3A3prime_partial%20len%3A35%20%28-%29
asmbl_1 .       five_prime_utr  108     1180    .       -       .       ID=asmbl_1|m.6.utr5p1;Parent=asmbl_1|m.6
asmbl_1 .       exon    1       1180    .       -       .       ID=asmbl_1|m.6.exon1;Parent=asmbl_1|m.6
asmbl_1 .       CDS     1       107     .       -       .       ID=cds.asmbl_1|m.6;Parent=asmbl_1|m.6

asmbl_10        .       gene    1       666     .       +       .       ID=asmbl_10|g.56;Name=ORF%20asmbl_10%7Cg.56%20asmbl_10%7Cm.56%20type%3A5prime_partial%20len%3A38%20%28%2B%29
asmbl_10        .       mRNA    1       666     .       +       .       ID=asmbl_10|m.56;Parent=asmbl_10|g.56;Name=ORF%20asmbl_10%7Cg.56%20asmbl_10%7Cm.56%20type%3A5prime_partial%20len%3A38%20%28%2B%29
asmbl_10        .       exon    1       666     .       +       .       ID=asmbl_10|m.56.exon1;Parent=asmbl_10|m.56
asmbl_10        .       CDS     1       115     .       +       .       ID=cds.asmbl_10|m.56;Parent=asmbl_10|m.56
asmbl_10        .       three_prime_utr 116     666     .       +       .       ID=asmbl_10|m.56.utr3p1;Parent=asmbl_10|m.56

 

I want to use this output in GenemarkET. But genemarkET can not recognize this gff3 format. When I tried using more simpler format of PASA gff file like - 

Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    25534    25824    .    +    .    ID=align_121075;Target=asmbl_1 1 291 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    28201    28302    .    +    .    ID=align_121075;Target=asmbl_1 292 393 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    28407    28544    .    +    .    ID=align_121075;Target=asmbl_1 394 531 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    28701    28784    .    +    .    ID=align_121075;Target=asmbl_1 532 615 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    28917    29073    .    +    .    ID=align_121075;Target=asmbl_1 616 772 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    31377    31784    .    +    .    ID=align_121075;Target=asmbl_1 773 1180 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    45575    45809    .    -    .    ID=align_121076;Target=asmbl_2 376 610 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    46739    46951    .    -    .    ID=align_121076;Target=asmbl_2 163 375 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    47017    47154    .    -    .    ID=align_121076;Target=asmbl_2 25 162 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    47786    47809    .    -    .    ID=align_121076;Target=asmbl_2 1 24 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    58231    58327    .    +    .    ID=align_121077;Target=asmbl_3 1 97 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    61743    61875    .    +    .    ID=align_121077;Target=asmbl_3 98 230 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    61942    62137    .    +    .    ID=align_121077;Target=asmbl_3 231 426 +
Mp1087439_TGAC_V1.1_scaffold_1    assembler-Myzus    cDNA_match    62322    62513    .    +    .    ID=align_121077;Target=asmbl_3 427 618 +

GeneMarkET worked perfectly. Can somebody please help me to convert my earlier gff3 format in to later simpler format.

Thank you 

 
 
rna-seq transdecoder GenemarkET • 2.4k views
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So you want to convert gff3 to gff, have you checked previous posts? Convertion Of Gff3 To Gtf

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I tried this ... doesn't work

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