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How remove gaps from gff file?

Hello

Thank you so much for reading this post. First of all, I would like to say that I am very new to this area of bioinformatics.

I would like to know what tool (preferably using Anaconda) I could use to remove gaps from a GFF file, and how I could use it properly.

Thank you very much

genome sequence gene
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updated by Ram Ram • written by zion22 zion22

What do you mean by gap?

• 1 views • link
written by ATpoint ATpoint

like "", "-", " ", "" or "?"

• 1 views • link
written by zion22 zion22

Please post a selection of the file. head -n 20 file.gtf

• 1 views • link
written by ATpoint ATpoint

hi, 

scaffold_1      JGI     exon    3645    3780    .       -       .       name "estExt_Genewise1.C_10001"; transcriptId 643699
scaffold_1      JGI     CDS     3673    3780    .       -       0       name "estExt_Genewise1.C_10001"; proteinId 643589; exonNumber 9
scaffold_1      JGI     stop_codon      3673    3675    .       -       0       name "estExt_Genewise1.C_10001"
scaffold_1      JGI     exon    3851    4004    .       -       .       name "estExt_Genewise1.C_10001"; transcriptId 643699
scaffold_1      JGI     CDS     3851    4004    .       -       1       name "estExt_Genewise1.C_10001"; proteinId 643589; exonNumber 8
scaffold_1      JGI     exon    4083    4210    .       -       .       name "estExt_Genewise1.C_10001"; transcriptId 643699
scaffold_1      JGI     CDS     4083    4210    .       -       0       name "estExt_Genewise1.C_10001"; proteinId 643589; exonNumber 7
scaffold_1      JGI     exon    4270    4397    .       -       .       name "estExt_Genewise1.C_10001"; transcriptId 643699
scaffold_1      JGI     CDS     4270    4397    .       -       2       name "estExt_Genewise1.C_10001"; proteinId 643589; exonNumber 6
scaffold_1      JGI     exon    4463    4737    .       -       .       name "estExt_Genewise1.C_10001"; transcriptId 643699
scaffold_1      JGI     CDS     4463    4737    .       -       1       name "estExt_Genewise1.C_10001"; proteinId 643589; exonNumber 5
• 1 views • link
updated by GenoMax GenoMax • written by zion22 zion22

But this example doesn't include some of your "gaps", does it?

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written by finswimmer finswimmer

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