Gff files

This page describes how to create an annoated genome submission from GFF3 or GTF files, using the beta version of our process. Note that you can always use GenBank's standard 5-column feature table see Prokaryotic Annotation Guidelines or Eukaryotic Annotation Guidelines as input. The basic characteristics of the file formats are described at:.

Several basic validators are available to verify that a GFF3 file is syntactically valid:. Note these standalone validators will not detect all formatting and annotation issues, and the GenBank annotation submission software is tolerant of some common GFF3 formatting issues, but they can be useful for initial testing, especially if an input file isn't working as expected.

An additional set of rules, specific attributes equivalent to INSDC qualifiers , and automatic processing are utilized for submission of annotated genomes to GenBank. These additions are:. For assemblies already in GenBank, seqids will be matched to their corresponding accessions if they are the same as what was used in the original submission. Furthermore, whereas the GFF3 specifications require that all rows of a multi-exon CDS feature use the same ID, some commonly used software deviates from this requirement.

To allow for deviations from the specifications, for eukaryotes the GenBank software assumes that multiple CDS rows with the same Parent attribute represent parts of the same CDS feature. Consequently, if a product is only on the mRNA or gene, the CDS will be automatically named 'hypothetical protein' and that name will be copied to be the product name of the corresponding mRNA.

In this case the. Commonly used types are:. Some SO types may need to be changed before processing in order to be properly recognized: [a] all gene features should use "gene". Use "transcript" instead. Feature types that aren't recognized will be automatically dropped and reported in the log file. Feature types that are always ignored so not reported in the log file are:. These are genes that do not encode the expected translation, for example because of internal stop codons. They can be provided either by including both or neither of them.

Specifically [a] and [b], OR just [c]:. Further details are available in the eukaryotic annotation guidelines. These qualifiers do not appear in the flatfile view, so if the GFF3 IDs are meant to be seen in that view, then they should be copied into a 'note' attribute with the appropriate formatting.

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. The command line for such a quick cleanup and a quick visual inspection of a given GFF file could be:.

This will show the minimalist GFF3 re-formatting of the transcript records found in the input file annotation. The -E option directs gffread to "expose" display warnings about any potential issues encountered while parsing the input file.

For this operation a fasta file with the genomic sequences have to be provided as well. For example, one might want to extract the sequence of all transfrags defined as transcripts or transcript fragments that result from the assembly process assembled from a StringTie or Cufflinks assembly session. This can be accomplished with a command line like this:. The file genome. This also requires that every contig or chromosome name found in the 1st column of the input GFF file transcript.

Remember, different programs may use GFF files for different purposes, so you may need to try out a few of them to be able to open your specific file. Try a universal file viewer like Free File Viewer.

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