Skip to content

GeneHancer for AnnotSV v3.4.5 #291

@thedam

Description

@thedam

When running a new version v3.4.5 there is no WARNING message, that GeneHancer data is not set (like it was before, while running AnnotSV for the first time after installation)
Now, when run AnnotSV v3.4.5 I can see message:

...listing of the annotations to be realized (July 22 2025 - 17:36)
        ...CytoBand annotation
        ...Genes annotation
                ...RefSeq annotation
        ...Regulatory elements annotations
                ...Promoter annotations
                ...EnhancerAtlas annotations
                ...GeneHancer annotations

So apperently AnnotSV uses GeneHancer?
I don't see any GeneHancer files here:

AnnotSV/share/AnnotSV/Annotations_Human/FtIncludedInSV/RegulatoryElements/GRCh38$ ls
ABC_ENSEMBL_GRCh38.sorted.bed  EA_RefSeq_GRCh38.sorted.bed   MPRA_ENSEMBL_GRCh38.sorted.bed           miRTargetLink_RefSeq_GRCh38.sorted.bed     promoter_3500bp_ENSEMBL_GRCh38.sorted.bed
ABC_RefSeq_GRCh38.sorted.bed   GH_ENSEMBL_GRCh38.sorted.bed  MPRA_RefSeq_GRCh38.sorted.bed            promoter_1500bp_ENSEMBL_GRCh38.sorted.bed  promoter_500bp_ENSEMBL_GRCh38.sorted.bed
EA_ENSEMBL_GRCh38.sorted.bed   GH_RefSeq_GRCh38.sorted.bed   miRTargetLink_ENSEMBL_GRCh38.sorted.bed  promoter_2500bp_ENSEMBL_GRCh38.sorted.bed  promoter_500bp_RefSeq_GRCh38.sorted.bed

Also this instruction seems to have no effct:

Image

Is the GeneHancer indeed used?

Best regards
DamianL

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions