[maker-devel] How to remove contigs from GFF file

[Daniel Ence]

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 <eennadi at gmail.com> 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.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>_______________________________________________
> maker-devel mailing list
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