How to remove contigs from GFF file

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How to remove contigs from GFF file

Emmanuel Nnadi
Hello,

I need to remove sequences from my GFF file can someone help me with command line for such removal

ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>  [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

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Re: How to remove contigs from GFF file

Daniel Ence-2
Hi Emmanuel, can you send the command that produced the error? If you need to remove certain scaffolds or contigs from a gff3 file, you can use grep to to filter out certain scaffolds like this “grep -v “scaffold_name” gff3_file”. 

~Daniel



On Oct 26, 2017, at 5:34 PM, Emmanuel Nnadi <[hidden email]> wrote:

Hello,

I need to remove sequences from my GFF file can someone help me with command line for such removal

ERROR: valid [SEQ_FEAT.FeatureBeginsOrEndsInGap] Feature begins or ends in gap starting at 17625 FEATURE: Gene: CR513_57782 <46071>  [lcl|contig_14719:17653-17724] [lcl|contig_14719: delta, dna len= 17790]
ERROR: valid [SEQ_INST.ShortSeq] Sequence only 2 residues BIOSEQ: gnl|aceprd|CR513_62412: raw, aa len= 2

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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