Activity for Ken

  • Ken Ken posted a comment on discussion General Discussion

    Can be found at https://github.com/czc/nb_distribution

  • Ken Ken posted a comment on discussion General Discussion

    you should export the path to the novoBreak_distribution directory. The command should be "export PATH=$PATH:/data/tmp/huebnerj/novoBreak_distribution_v1.1.3rc".

  • Ken Ken posted a comment on discussion General Discussion

    If there is no normal control, a simulated normal bam file (no coverage need) can be used to meet the interfaces of novoBreak. But the results would be both somatic and germline events. You can use wgsim to simulate raw reads from reference and align them using bwa to generate a bam file as "normal".

  • Ken Ken posted a comment on discussion General Discussion

    The source code of novoBreak is on the SourceForge already. Simply use "git clone https://git.code.sf.net/p/novobreak/git novobreak-git && cd novobreak-git && make" and copy the binary of novoBreak to replace the "novoBreak" in novoBreak_distribution_v1.1.3rc should be fine. If the software in the novoBreak_distribution_v1.1.3rc directory cannot use due to Linux environment (such as samtools), simply download the source and compile, install and copy to the novoBreak_distribution_v1.1.3rc directory...

  • Ken Ken posted a comment on discussion General Discussion

    Hi Wenkai, You may try the inherent second filter filter_sv2.pl. Or a tip you may...

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