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OpenGene / GeneFuse

Gene fusion detection and visualization
MIT License
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Can not get the fusions with the testdata #31

Open kingyang728 opened 3 years ago

kingyang728 commented 3 years ago

Can not detect the fusions with the test data,is anyone can help me? all the testdata is from the git and http://opengene.org/dataset.html

Here is my shell command: ./genefuse -r Homo_sapiens_assembly19.fasta -f genes/cancer.hg19.csv -1 ./testdata/genefuse.R1.fq.gz -2 ./testdata/genefuse.R2.fq.gz -h report.html > result 12:17:45 start with 4 threads 12:18:1 mapper indexing done 12:18:6 sequence number before filtering: 0 12:18:6 removeByComplexity: 0 12:18:6 removeByDistance: 0 12:18:6 removeIndels: 0 12:18:53 matcher indexing done 12:18:53 removeAlignables: 0 12:18:53 found 0 fusions 12:18:53 done

granek commented 3 years ago

I had the same problem! The fusion files in the repo are not compatible with the NCBI version of hg19 that is linked in the README. The fusion files have chromosome names that start with "chr", but the genome from NCBI just uses the chromosome number (e.g. "chr15" vs "15").

The easiest fix is to download hg19 from UCSC: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz