Questions tagged [gff3]
Generic Feature Format version 3, a common tab-delimited plain-text format for annotating genes and other genomic features.
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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 ...
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How to extract sequences of a specific gene from genomes, with genomes' .fna, .gff and results from KofamScan?
I am trying to do alignment among orthologs and paralogs of a gene but I encountered some problems. I have came up with a workflow, but the sequences I extracted are not correct. They are of hugely ...
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Improving conversion of abricate tsv file to gff3 file
Since such a neat solution (abricate tsv to gff3) was provided by Steve, here are few other steps that I am looking to add so that the script progress to logical maturity to be usable by many others.
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Convert Abricate output tsv file to gff3 format
I have a tsv file generated from abricate (https://github.com/tseemann/abricate). I need to convert them to gff3 format with certain columns retained, certain columns reordered, while other columns ...
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How to wget a gff from NCBI database?
Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here.
However, I do not see ...
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What does it mean when a gene and its transcript have opposite orientations in a GFF3 file?
I was working with a given GFF3 file, and I observed that some transcripts have orientation opposite to their transcripts. Here is a snippet:
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Stringtie/DEprep.py 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 -> DEprep.py workflow.
DEprep.py outputs a ...
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Perl convert GFF3 file
I have the following GFF3 file which I would like to convert to ZFF file with the below script:
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Edit end column in GFF3 file
I am trying to edit the "end" of my sequences in a GFF3 that contains 10000 sequences (so I do not want to do it manually). I want to add 30 residues to every single fragment. How can I do ...
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Counting the number of gene isoforms in a GFF3, is this method correct?
Recently I've been tasked to count the numbers of gene isoforms for each locus in a .gff3 file. I'm still doing my first steps in biology and bioinformatics, so I ...
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Create GFF3 feature exporter
Problem Statement
The GFF3 format is a commonly-used one in bioinformatics for
representing sequence annotation. You can find the specification
here:
http://www.sequenceontology.org/gff3.shtml
The ...
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Get gene sequence based on the annotation
I've got the reference genome with Python like so:
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renaming IDs in gff3 with BCBio.GFF
I wrote a script which should changes IDs in a GFF3 file. Unfortunately, the below script has two problems.
It attaches the new ID to Parent which leads that ...
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Existing tool for converting gff3 to genbank (gbk)
I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ which can perform this task, but my files (...
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Modifing a GFF3 file and writting to a new file
I modified the GFF3 file with the below code:
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Adding an attribute to GFF3 file
I failed to add Note=Gene description to mRNA attribute with the below code:
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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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Transcript Coordinate Ranges to Genomic Coordinates
I have 2 GFF3 files:
Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space.
Features using chromosome IDs as the landmarks. i.e. "exon" ...
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In GFF3, annotating more than one protein-coding gene (i.e. polycistronic) contained in a eukaryotic mRNA
Below is an example of a simple GFF3 file:
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Infer missing UTR features in GFF3 file
I am working on a GFF file that is missing the 5'UTR and 3'UTR information. For example:
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Transferring genomic features on new coordinates
I have a eukaryotic genome for which an updated sequence for a chromosome was recently obtained. I want to map RNAseq reads on the genome (and perform other downstream analyses) and would like to use ...
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Which identifier do I have to use when I want to add a ##Fasta section to a gff?
I have a gff file like this
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Can exons be located outside of the coding sequence?
I have a gff file like this (I edited the name):
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How to provide a GFF/GTF file to Chromonomer
I am trying to use Chromonomer. It should be possible (according to the software page and a paper) to add a GFF/GTF file to the analysis.
Alas, neither the built-in help nor some light source code ...
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How to extract / convert gff3 CDS sequences to multifasta
I would like to extract all the CDS from a batch of genomes. I have found a perl script from BioStars but this does not seem to work for me. I would preferably like to have a script/ method which will ...
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How to convert BED to GFF3
I would like to convert a BED format to GFF3.
The only useful tool that I could find via a google search seems to be Galaxy, ...
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How GFF3 attributes (9th column) varies from one gene prediction algorithm to another
GFF3 files are in tabular format with 9 fields per line, separated by tabs. The first 8 fields share almost same data structure, but the 9th field varies a lot depending on feature type and gene ...
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Does Prokka or gff3 change the sequence / subject ID of fasta files?
I used prokka to create a database for some fasta files but I noticed a strange difference between the prokka and fasta files. Normally the seqid for the gff3 output for prokka has seqid's that match ...
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How to convert GFF3 to GTF2
I would like to convert a file in gff3 format to a gtf2.2 format.
The reason why I would like to do this is: I have a set of ...
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How to dump genes from GenBank in GFF3 format?
This question has also been asked on BioStars
If I look at this record in GenBank I see about 6k genes:
https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts
I'd really like to be able to ...
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What kind of "gff" format does bioawk parse?
I was wondering if I could use the gff parsing capability of bioawk to facilitate the parsing of gtf files, and I looked at the following help message:
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Annotation format design
Bashing file formats is a favorite pastime in bioinformatics, and annotation file formats such as GFF and BED seem to get special attention. A lot of this frustration stems from community's shockingly ...
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