gtf

gtf: Command not found.
This utility does not exist as a standard Linux command and will typically result in a 'command not found' error upon execution.

The command gtf is not a standard or commonly recognized utility in most Linux distributions. It is highly probable that the query refers to the Gene Transfer Format (GTF), which is a text-based file format used extensively in bioinformatics to describe gene and genomic feature annotations. While numerous specialized bioinformatics tools exist to process GTF files (e.g., for gene quantification, transcriptome assembly, or format conversion), there is no generic Linux command simply named gtf that performs these operations by default. The term 'GTF' exclusively refers to the file format, not an executable program itself in standard Linux environments.

This command does not exist as a standard Linux utility. Users seeking to process GTF files should consult documentation for specific bioinformatics tools designed for reading, parsing, converting, or analyzing genomic annotations stored in this format. Attempting to run 'gtf' will only yield an error.

The Gene Transfer Format (GTF) is a specific tab-separated text file format primarily used in genomics to annotate gene structure. It shares similarities with the GFF3 format but has stricter conventions, particularly for gene and transcript features. A GTF file typically consists of nine columns:
1. Chromosome name
2. Source (e.g., Ensembl, Havana)
3. Feature type (e.g., 'exon', 'CDS', 'start_codon')
4. Start coordinate
5. End coordinate
6. Score (usually '.' or a numeric value)
7. Strand ('+' or '-')
8. Frame (0, 1, 2 for CDS features, '.' otherwise)
9. Attributes (a semicolon-separated list of 'key "value"' pairs, including 'gene_id' and 'transcript_id').

There is no documented history for a standard Linux command named gtf, as it is not part of common Linux distributions. The acronym 'GTF' itself originates from the bioinformatics community, specifically describing a well-defined format for genomic annotations, first introduced as part of the Ensembl project specifications.

gffread(1) (A utility often used for converting and manipulating GFF/GTF files, part of the StringTie/Cufflinks suite.), bedtools(1) (A versatile suite of tools for genomic feature manipulation, which can interact with GTF files for various operations like intersecting or merging.), featureCounts(1) (A program for quantifying reads against genomic features defined in GTF or GFF files.), stringtie(1) (A tool for transcriptome assembly and quantification that utilizes GTF annotations.)