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OpenGene / GeneFuse

Gene fusion detection and visualization
MIT License
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No fusion generated using demo fastq files #9

Open foxchase opened 6 years ago

foxchase commented 6 years ago

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

sfchen commented 6 years ago

I have updated the demo dataset, which contains a valid EML4-ALK fusion with ultra-high frequency.

Please download it again from: http://opengene.org/dataset.html

foxchase commented 6 years ago

Hi Shifu, I downloaded the new demo data and tried again with no fusion generated, the same issue. Additionally, I tried the gen_fusion_file.jl file and got a lot errors, please see attachments. Would you please check the version that you use is the same as that on the github. Many Thanks. error_Julia.txt TRFPgenes.txt

sfchen commented 6 years ago

Could you let me know how many lines do R1.fq and R2.fq have? They should be 15000000 lines for each file.

For the second issue. Which genes do you want to include? I can generate the CSV file for you. Julia language is evolving so fast, so the package may encounter compatible problems.

foxchase commented 6 years ago

Hi Sifu, Yes, R1 and R2 each has 15,000,000 lines. I ran fusion analysis for your R1 and R2, and there are ALK-EML4 fusion and others in the R1/R2 fastq files; that is no problem for the R1 and R2 fastq file. Is the version of GeneFuse that you use different from the one you posted? I work on illumina RNA Fusion Panel, attached is the gene list of the Panel, I need hg19 for the CSV file. It is greatly appreciated for doing that. Additionally, please let me know if you need test (positive) fastq files of that panel. TRFPgenes.txt