Customized Mouse Genome Annotation from Ensembl 102

Ensembl version 102 (mm10) annotations were filtered to remove readthrough transcripts and non-coding transcripts from protein-coding genes. Overlapping genes with the same name were merged under a single gene ID to reduce ambiguous read mapping. This version retains genes on contigs and includes CDS information, as described in an accompanying bash script.

Use Cases

• Gene expression quantification based on a filtered set of protein-coding transcripts.
• Read alignment and mapping using a GTF file designed to avoid ambiguous gene assignments.
• Comparative genomics analysis leveraging the standardized Ensembl mm10 build.
• Transcriptome assembly and annotation referencing the included CDS (coding sequence) information.

Strengths

• Derived from the authoritative Ensembl version 102 (mm10) genome build.
• Includes specific filtering steps (removal of readthrough and non-coding transcripts) to improve accuracy for certain analyses.
• Merges overlapping genes with identical names to a single ID, reducing mapping ambiguity.

Limitations

• Key metadata such as row count, file size, and specific column names are not provided by any source.
• The exact date of the last update is unknown, limiting assessment of freshness.
• Sources provide slightly varying descriptions, with some omitting mention of contig genes and CDS information.

Provenance

Source

École Polytechnique Fédérale de Lausanne (EPFL), author Lucille Lopez‐Delisle.

Collection Method

Custom filtering and processing of the Ensembl 102 mm10 GTF file, with procedure documented in a bash script.