fusioncatcher
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ndaniel
Finder of Somatic Fusion Genes in RNA-seq data
Changed #!/usr/bin/python for #!/usr/bin/env python, because if it is left in that way it won't complete execution of the fusioncatcher-build.py script sh: 1: add_custom_gene.py: not found ERROR: Workflow execution failed...
I test fusioncatcher using the test fq files: ``` http://sourceforge.net/projects/fusioncatcher/files/test/reads_1.fq.gz http://sourceforge.net/projects/fusioncatcher/files/test/reads_2.fq.gz ``` for the glibc error reason, I can only run it through a singularity image: `singularity exec -B /mnt/lustre/user/wubin/01.Program/Scripts/02.software/Fusioncatcher/fusioncatcher:/mnt,/mnt/lustre/user/wubin/01.Program/Scripts/02.software/Fusioncatcher/fusioncatcher/test/fq_dir:/tmp,/mnt/lustre/user/wubin/01.Program/Scripts/02.software/Fusioncatcher/fusioncatcher/test/output:/opt...
issue #194 quick fix or else the tools needs to be removed from the documentation and this install script.. Don't pull because I didn't test the bootstrap script.
I am writing to report an issue I encountered while running FusionCatcher. During the process, I received the following error message:IOError: [Errno 2] No such file or directory: '/mnt/sdc/wwDatas/RGC_fusion/GSE236027_data/res/fusionca_res/SRR25052121/reads_ids_unmapped.txt' [fusioncatcher.log](https://github.com/user-attachments/files/16671286/fusioncatcher.log)...
Dear fusion catchers, While building the indexes for fusion catcher we stumbled upon an issue that may be derived from a change in the FTP structure that break some assumptions....
I am using FusionCatcher downloaded and installed via miniforge3 according to the manual at https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md All seems to be working fine, thank you, but the output file misses two last...
Hi, I encountered an error while trying to download the genome of Canis lupus familiaris from the Ensembl server using this commend. `fusioncatcher-build.py -g canis_lupus_familiaris -o genome_build` As a result,...
Is it possible to run fusioncatcher on gencode human reference or using a human reference previously downloaded?
This script seems to be running very long, like 3 days per sample. Is this expected? ``` VIRT RES SHR S %CPU %MEM TIME+ COMMAND 71.9g 70.3g 1916 S 1.6...
Hi, I am trying to look for an example TSV from FusionCatcher because I need to know in cases like this `GOPC;ROS1` `GOPC;ROS1`, whether the gene names will be separated...
