Is using the webapp link above to get fusions annotations give the same output results as writing and running a bash script like this below as I am getting runtime errors with it
DATABASE="./agfusion.homo_sapiens.111.db"
Hard-coded fusion information for DNAJB1-PRKACA:
Gene 5': DNAJB1
Gene 3': PRKACA
5' junction coordinate: chr19:14518139 → numeric 14518139
3' junction coordinate: chr19:14107409 → numeric 14107409
GENE5PRIME="DNAJB1"
GENE3PRIME="PRKACA"
JUNCTION5PRIME="14518139"
JUNCTION3PRIME="14107409"
echo "Annotating fusion: ${GENE5PRIME}-${GENE3PRACA}"
echo "Using database: ${DATABASE}"
echo "5' breakpoint: ${JUNCTION5PRIME}"
echo "3' breakpoint: ${JUNCTION3PRIME}"
Run AGFusion annotation.
agfusion annotate
--gene5prime "${GENE5PRIME}"
--gene3prime "${GENE3PRIME}"
--junction5prime "${JUNCTION5PRIME}"
--junction3prime "${JUNCTION3PRIME}"
-db "${DATABASE}"
-o "${OUTPUT_DIR}/${GENE5PRIME}-${GENE3PRIME}"
echo "AGFusion annotation complete."
Is using the webapp link above to get fusions annotations give the same output results as writing and running a bash script like this below as I am getting runtime errors with it
DATABASE="./agfusion.homo_sapiens.111.db"
Hard-coded fusion information for DNAJB1-PRKACA:
Gene 5': DNAJB1
Gene 3': PRKACA
5' junction coordinate: chr19:14518139 → numeric 14518139
3' junction coordinate: chr19:14107409 → numeric 14107409
GENE5PRIME="DNAJB1"
GENE3PRIME="PRKACA"
JUNCTION5PRIME="14518139"
JUNCTION3PRIME="14107409"
echo "Annotating fusion: ${GENE5PRIME}-${GENE3PRACA}"
echo "Using database: ${DATABASE}"
echo "5' breakpoint: ${JUNCTION5PRIME}"
echo "3' breakpoint: ${JUNCTION3PRIME}"
Run AGFusion annotation.
agfusion annotate
--gene5prime "${GENE5PRIME}"
--gene3prime "${GENE3PRIME}"
--junction5prime "${JUNCTION5PRIME}"
--junction3prime "${JUNCTION3PRIME}"
-db "${DATABASE}"
-o "${OUTPUT_DIR}/${GENE5PRIME}-${GENE3PRIME}"
echo "AGFusion annotation complete."