Users' questions

Is GFF3 the same as GFF?

Is GFF3 the same as GFF?

General Feature Format (GFF) is a tab-delimited text file that holds information any and every feature that can be applied to a nucleic acid or protein sequence. GFF3 has 9 required fields, though not all are utilized (either blank or a default value of ‘. …

How do I merge GFF files?

Upload the annotation files to the Annotation Files Merger Click on the “Annotation Files Merger” link under the “Resources & Tools” section. Under the “File Type” field, select the type of files you would like to merge (i.e. GFF, transcript sequence, peptide sequence, or VCF files).

How do I open a GFF3 file?

GFF Viewer can be opened with the context menu option in the File Manager when selecting a GFF file and using the context menu option Show in GFF Viewer from the table when exploring a GFF file.

What is genomic GFF?

A General Feature Format (GFF) file is a simple tab-delimited text file for describing genomic features. There are several slightly but significantly different GFF file formats. IGV supports the GFF2, GFF3 and GTF file formats.

When should you use a GTF file?

The Gene transfer format (GTF) is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format (GFF), but contains some additional conventions specific to gene information.

What is in a SAM file?

The SAM format consists of a header and an alignment section. The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. SAM files can be analysed and edited with the software SAMtools.

How to convert GFF3 file to gtf2 format?

The gff3 file was created as output of GMAP, and contains the transcripts as found by alignment to the reference (specifying option -f gff3_match_cdna ). [Edit: what I found out a poteriori, is that this format is not a standard gff3, thus the conversion is not trivial…] Here is the beginning of the gff3 file I tried to convert:

How to extract sequences from a GFF file?

Extract sequences from specific regions of genome based on gff file. Incorporation of is contributed by Han Lin which uses simple data structures to parse a [ GFF3] file into a structure composed of simple python [ dict] and [ list ].

How is the gffread utility used in GFF?

Thus the gffread utility can be used to simply read the transcripts from the file, and optionally print these transcripts back, in either GFF3 (default) or GTF2 format (with the -T option), while discarding any non-essential attributes, optionally fixing some potential issues with the input file (s).

How to specify a FASTA file in GFF3?

Fasta file: specify the file name with the -f argument. This file must be the Fasta file that the GFF3 seqids and coordinates refer to. For more information, refer to the GFF3 specification. Output prefix: specify with the -o argument.