GeneFuse
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OpenGene
Gene fusion detection and visualization
No fusion detected with the demo data genefuse -r hg19.fasta -f genes/druggable.hg19.csv -1 R1.fq -2 R2.fq -h report.html > result
amar@amar-Virtual-Machine:~/GeneFuse$ ./genefuse -1 testdata/R1.fq -2 testdata/R2.fq -r Homo_sapiens_assembly19.fasta -f genes/cancer.hg19.csv 22:53:5 start with 4 threads 22:53:9 mapper indexing done 22:53:9 sequence number before filtering: 0 22:53:9 removeByComplexity: 0 22:53:9 removeByDistance:...
1, COSMIC curated fusions 2, can be transcribed or not 3, supporting reads number
Read1 ``` @name1 AGGGTTACCTGAGGATCGAATGAATTGAAATGTGTAAATTGCCGAGCACGTAGTAACCATGCAACAAGTGTTAGCTCCTATTATCCTGTCCCTTTGAGGGATGGCACCATATGGGGACACAGTGTGTGCTGCCATCTCCCTTCTACCGGC + EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE ``` Read2 ``` @name1 TGGGCCCTCCCTCCCAAGCACTGGAGGAGGTACTCGTTCTGTGGGCCGGGGCCCCTCCCTCCTGAGCACTGGAGGAGGCACTTGTTCTGTGGGCCACGGCCCCTCCCTCCCCAGCACTGGAGGAGGCACTGGTTGTGTGGGCCCTGGCTC + EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE ```
Can I use this soft to call fusion gene from RNAseq data? Could anyone give me some advice? thanks so much !
Multiple runs show different unique read count. `vec` is sorted differently a bit per run. Some `Match`s have the same `read_break` and `seq.length()`. This was found with hg19.fa, druggable.hg18.csv, test...
In indexer.cpp:347 ```cpp ... // or smaller positive if contig is the same if(left.startGP.contig == right.startGP.contig && abs(left.startGP.position) < abs(left.startGP.position)) return true; else return false; ... ``` Your intention was...
I have a sample with BCL2-IGH verified by FISH. There are lots of reads to support viewed by IGV. the pictuers is as follows. I am running with default parameters，and...
