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I noticed some inconsistencies between public cBioPortal and MSK cBioPortal regarding structural variant data. I'm also not able to pull structural variant data anymore via the API endpoint for these …
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I am using deeptools bamCoverage to analyze short (35-80bp) paired end fragments. All reads in my bam file are properly paired based on samtools flagstat and Picard. Yet bamCoverage extends some a…
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I have observed cases where my dual UMIs can get swapped during amplification steps in library prep, resulting in two consensus sequences which align to the same start/stop position but share the half…
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Hi,
After some testing I am trying to download another instance of ITSFASTR so I can analyze real data. However, when I execute the code after having modified the samplesheet.csv and the config.yaml …
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Hello again!
I was able to run the script and everything was correct ! The problem that I face is that I trying to interprect was is the biological meaning of the correlation and rank values. Despit…
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Looking at a few cfDNA samples across different runs, we've noticed instances where the meth_qual distribution can vary widely quite a bit. Eg. some samples are strongly piled up near 0 or 255, and ot…
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I have just started exploring use of DMRcate for DMR detection but have concerns about the approaches dmrcate offers for ranking DMRs. DMRcate offers Fisher's combination, Stouffer's combination, and …
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The code attempts a `full join` here:
https://github.com/cruk-mi/mesa/blob/212a791cb4da2d2d2c099c4ef53b4b71d5f1ee65/R/combineQsets.R#L193
But, when joining large `qseaSets`, the result is too mu…
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Thank you for the amazing toolbox! I have noted something odd in the scripts generated to run lofreq call by makeSomaticScrtipts.py
Running 'makeSomaticScripts.py single:
```
#!/usr/bin/bash
hom…