User: poisonAlien
poisonAlien • 3.0k
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Cancer genomics
Posts by poisonAlien
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... You are almost there. You just need to copy/move the binary to a `PATH` (e.g; `/usr/local/bin`) or to a directory under `PATH`. ...
written 6 weeks ago by
poisonAlien • 3.0k
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... Thanks, @genomax and @ATpoint
I have updated the repository. ...
written 7 weeks ago by
poisonAlien • 3.0k
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... Thanks for testing and I am glad that you were able to make it work. I will make available the binaries soon :)
edit: centOS and macOS binaries for bwtool are included in the repository. Thanks for the suggestion. ...
written 7 weeks ago by
poisonAlien • 3.0k
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... I have tested quite throroughly on Ubuntu and CentOS. It works with no issues. Also, I do have a compiled version of bwtool on my mac (10.15.2), and I could not reproduce your errors. I guess opening an issue on `libbeato` might help to speed up debugging.
edit: I am happy to share the bwtool mac b ...
written 7 weeks ago by
poisonAlien • 3.0k
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... Try these [instructions](https://github.com/CRG-Barcelona/bwtool/issues/49#issuecomment-604477559) for bwtool compilation. It should work. Copied below as well.
git clone 'https://github.com/CRG-Barcelona/bwtool'
git clone 'https://github.com/CRG-Barcelona/libbeato'
git clone https://g ...
written 7 weeks ago by
poisonAlien • 3.0k
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... If you are working with chip-seq or atac-seq or any assays resulting in bigWig files, one of the common visualizations is to generate track plots displaying signal intensities across genomic loci. Libraries in R like [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html) facilitates s ...
written 7 weeks ago by
poisonAlien • 3.0k
• updated
6 weeks ago by
Sael • 20
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... If I have to explain technicalities of PCA to a biologist, [this][1] is where I would start.
[1]: https://www.youtube.com/watch?v=_UVHneBUBW0 ...
written 2.3 years ago by
poisonAlien • 3.0k
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... To answer your question in a simple sentence - In an ideal scenario, variants with VAF around 50% is fully clonal. Since most somatic mutations tend to be heterozygous, a clonal mutation would have an allele frequency of 50%. Anything below ~45/40% would be a sub-clonal.
But it also depends on your ...
written 2.3 years ago by
poisonAlien • 3.0k
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Comment:
C: TMB Tumor Mutation Burden
... I believe standard WXS capture sizes are around 50 mb. (eg; Agilent sure select) ...
written 2.9 years ago by
poisonAlien • 3.0k
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... I am not sure if I understand teh question correctly. But, you should look at one of those multi region WXS/WGS studies. Somatic mutation profile varies a lot within the bulk tumor based on biopsy site. So its pretty heterogeneous. ...
written 2.9 years ago by
poisonAlien • 3.0k
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