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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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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2answers
51 views

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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Using galaxy tool htseq_count for lncRNA in wheat reference genome

My group wants to use Galaxy's htseq_count to map reads from a BAM file onto the IWGSC v1.0 lncRNA GFF file however we have encountered several difficulties. Specifically, there are many lines for ...
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3answers
121 views

Modifing a GFF3 file and writting to a new file

I modified the GFF3 file with the below code: ...
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1answer
40 views

Adding an attribute to GFF3 file

I failed to add Note=Gene description to mRNA attribute with the below code: ...
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4answers
148 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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2answers
315 views

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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4answers
81 views

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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3answers
434 views

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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2answers
152 views

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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2answers
100 views

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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3answers
558 views

Can exons be located outside of the coding sequence?

I have a gff file like this (I edited the name): ...
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1answer
62 views

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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4answers
4k views

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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4answers
2k views

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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1answer
567 views

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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1answer
121 views

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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2answers
2k views

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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2answers
315 views

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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1answer
157 views

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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4answers
196 views

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 ...