raw_Homo_sapiens.GRCh37.74: Homo_sapiens.GRCh37.74_subset.gtf

In chimeraviz: Visualization tools for gene fusions

Description

Homo_sapiens.GRCh37.74_subset.gtf

Homo_sapiens.GRCh37.74_subset.gtf

The Homo_sapiens.GRCh37.74.gtf file is a subset version of the Ensembl Homo_sapiens.GRCh37.74.gtf file, located here: ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens. This gtf file contains transcripts for the partner genes in two of the fusion transcripts from the deFuse example data provided with this package: The fusion transcript with cluster_id=5267, and the fusion transcript with cluster_id=11759.

The file is the result of running this command:

# grep "ENST00000373831\|ENST00000373832\|ENST00000373833\|ENST00000398958\|ENST00000411533\|ENST00000419074\|ENST00000427469\|ENST00000429051\|ENST00000430407\|ENST00000434290\|ENST00000478232\|ENST00000486790\|ENST00000370031\|ENST00000370032\|ENST00000402983\|ENST00000420055\|ENST00000483729\|ENST00000493676\|ENST00000382073\|ENST00000299665\|ENST00000382064" Homo_sapiens.GRCh37.74.gtf > Homo_sapiens.GRCh37.74_subset.gtf

The transcript names given in the command above are all transcripts available for the genes CLEC6A, CLEC4D, HENMT1, and RCC1 in Ensembl version 74.

Homo_sapiens.GRCh37.74.sqlite

The Homo_sapiens.GRCh37.74.sqlite file is the sqlite database that the Ensembldb package creates from the corresponding gtf file. It was created using this command:

# ensDbFromGtf( # gtf = "Homo_sapiens.GRCh37.74_subset.gtf", # organism = "Homo_sapiens", # genomeVersion = "GRCh37", # version = 74)

chimeraviz documentation built on Jan. 19, 2021, 2 a.m.