GeneFuse

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Fusion-making .py script does not take into account gene orientation

8

Thanks for creating this tool! I have noticed that the `scripts/make_fusion_genes.py` reports wrong order of exons for genes in '-' orientation, which results in considering some fusions as untranscribed and...

nvolkovaGEL

make: *** No rule to make target 'install'. Stop.

2

Need help to compile from source code. Got "make: *** No rule to make target 'install'. Stop." when sudo make install, in ubuntu 16.04 LTS Running binary without any error...

jrhaulung

primary transcripts used in fusion.csv

1

Hi, Developers Could you explain the exact meaing of "primary transcript" in fusion.csv. Does it mean the `longest transcript` or `pre-mature transcript` ? many thanks zhengxc

zhengxinchang

How to use GeneFuse to detect fusion for nanopore sequencing fastq?

1

Hi sfchen, I have installed genefuse and worked for the test data successfully. However, it did not work for nanopore fastq. Could you help me? Thank you! My command line...

pepenglp

gen_fusion_file.jl

2

Hi, the same issue with gen_fusion_file.jl for csv file preparation while using Julia 0.6 version. `ERROR: LoadError: UndefVarError: readstring not defined in detect at /home/ubuntu/julia/gen_fusion_file.jl:33 in main at /home/ubuntu/julia/gen_fusion_file.jl:22 while...

gerbarinov

error when creating fusion.csv file

3

Hi, I am trying to create the fusion.csv file using the script that you provide gen_fusion_file.jl but I get the error: ``` loading gencode grch38 ERROR: LoadError: KeyError: key "localfile"...

ericavalentini

the gen_fusion_file.jl script does not work because OpenGene can not be installed

4

Hi ! I would like to run the julia script on a list of genes to get the file fusion.csv but I have not managed to install OpenGene, here is...

yahiaBioinfo

如题，大概看了一下制作融合基因列表的jl脚本和文件。脚本仅仅支持hg19或hg38。我理解OpenGene的julia包里这俩人类基因组的外显子信息应该是有来源的，例如gtf文件。那么，我考虑可否通过gtf文件直接来制造候选的融合基因列表呢？

wangshun1121

how to see the version of genefuse?

1

Hi, I got the genefuse by git clone on the command line, and make, finally, I got the binary genefuse, but I can't find the version of it. How to...

ShannonDaddy

What is the minimum required read length?

2

I conducted a simulation. When my read length is 89bp, it outputs expected fusions. However when I use read length of 85bp. There are no results. The main change is...

billzt