Galaxy |

GTF2GeneList (version 1.52.0+galaxy0)

Ensembl GTF file:

Feature type for which to derive annotation:

Field to place first in output table:

Suppress header line in output?:

Comma-separated list of field names to extract from the GTF (default: use all fields):

Append version to transcript identifiers?:

For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes

Column to be used to fill empty values in other fields:

Only when output fields are defined, useful when you need to guarantee a value, for example a gene ID for a transcript/gene mapping.

Flag mitochondrial features?:

Comma-separated list of possible mitochondrial chromosome names (case insensitive):

Comma-separated list of possible mitochondrial biotypes (case insensitive):

Provide a cDNA file for extracting annotations and/ or possible filtering?:

For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)

What it does

Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. See https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.

You can also supply a fasta-format file of sequences, which can be filtered by identifier to match annotation and/or used a source of information for transcripts un-annotated in the GTF. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation).

Inputs

Ensembl GTF file

Outputs

Gene annotations in tsv.