Questions tagged [gff]

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Number of collinear genes are zero while running MCScanX

I am trying to do a synteny analysis using MCScanX. As per requirement I have done all by all blast between two sets of protein from two closely related species. And also prepared the gff file. The ...
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1 vote
2 answers
156 views

Extract only exon regions from GFF/GTF file with input bed regions

I have a bed file that contains a list of regions and I would like to extract only the exon regions from a GTF/GFF file that are contained in the given regions. Is there a simple command or tool that ...
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  • 195
8 votes
3 answers
275 views

How to import large .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently. All of these three ...
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  • 1,347
0 votes
1 answer
105 views

HTSeq-count is returning 0 for every gene, instead of expression value

(Ported from stack overflow) I'm trying to summarize gene count using htseq-count; and it's returning 0 counts at every gene. I'm not sure what I'm doing wrong; I think it has to do with the gene ...
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4 votes
4 answers
6k views

How to convert gff to gtf?

My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format? I am working on sequences from ...
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  • 121
3 votes
3 answers
299 views

GTF from consensus sequence

I am new to using bioinformatic tools and I was hoping this community could help clear something up for me. I need to generate a gtf file. My data are a set of complete HA genes for influenza B ...
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  • 33
3 votes
4 answers
224 views

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

I downloaded the annotation of the C. elegans genome in GFF3 format from Ensembl. I typed the following command, hoping to get the header of the file (lines starting with ...
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3 votes
4 answers
5k views

Can a gff file be converted to a fasta file?

I downloaded an annotated genome file in gff format here. I would like to use it for proteomics. Though I need it in fasta format. Is there any tool that converts gff to annotated fasta? I see the ...
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  • 1,181
7 votes
3 answers
1k views

Importing GFF file with Biopython

Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file? For example, ...
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