Questions tagged [gff]

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How can I convert a BED file to GTF/GFF with gene_ids?

Given a .bed (BED12), how can I convert it to GTF/GFF formats with gene_id attributes? What is the fastest way or available tools to do it? For example, given an input like this: ...
Alejandro Gonzales-Irribarren's user avatar
1 vote
0 answers

Extracting animo acid and nucleotide sequences from KofamScan output and codon alignment

I want to extract the amino acid sequences from KofamScan output, and my workflow is as attached in the picture: For the analysis I am doing, I need to get the animo acid sequences, align them, and do ...
Lily Li's user avatar
  • 23
3 votes
2 answers

Which candida albicans fasta and gff file should I use for alignment?

I downloaded the gff and fasta files for candida albicans from I want to use hisat2 to align some fastq files against it. There are ...
irritable_phd_syndrome's user avatar
1 vote
0 answers

conversion of a gbff file to a gff file

I want to get the annotations in gff format for a assembled genome. But for some species there is no available annotation in gff format in NCBI but only in gbff format. And I don’t know how to convert ...
Kishor Kumar Sarker's user avatar
1 vote
0 answers

Stringtie/ gene/transcript IDs are wrongly formatted

Hi my RNAseq workflow is ending up with wrongly formatted gene IDs (and separately transcript _IDs) after a Hisat2 ->samtools sort -> stringtie -> workflow. outputs a ...
RichardBJ's user avatar
  • 111
1 vote
1 answer

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 ...
Kishor Kumar Sarker's user avatar
1 vote
2 answers

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 ...
SBDK8219's user avatar
  • 195
9 votes
2 answers

How to import a large amount of .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 ...
0x90's user avatar
  • 1,427
0 votes
1 answer

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 ...
sdshinghal's user avatar
6 votes
4 answers

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 ...
Diango's user avatar
  • 151
3 votes
3 answers

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 ...
Lindsey's user avatar
  • 33
3 votes
4 answers

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 ...
Biomagician's user avatar
  • 2,459
3 votes
4 answers

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 ...
Soerendip's user avatar
  • 1,295
7 votes
3 answers

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, ...
Alex Summers's user avatar