Questions tagged [gff]

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8
votes
3answers
209 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 ...
3
votes
4answers
205 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 ...
4
votes
3answers
5k 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 ...
0
votes
1answer
72 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 ...
3
votes
3answers
268 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 ...
3
votes
4answers
4k 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 ...
7
votes
3answers
907 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, ...