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When I am running Philosopher (version 3.4.13) on a set of TMT10-MS3 samples, I am reaching the "label-free quantification step" and experiencing the following error message:
```
...
time="10:23:…
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Hi, I'm following the pipeline for TMT analysis tutorial to perform an analysis on files which I have converted to mzML from raw using MSConvert on linux. I am getting the following error at the Pepti…
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Hi, further to [another issue](https://github.com/Nesvilab/philosopher/issues/139) I was discussing which I now believe to be resolved, I am using the TMT pipeline to analyse databases that I am downl…
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##### System information (version)
- OpenCV => :grey_question: 4.4
- Operating System / Platform => :grey_question: Windows 64 Bit
- Compiler => :grey_question: Visual Studio 2019
##### Det…
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my command is:
`$VEP/vep --fork 8 --refseq --use_given_ref --force_overwrite --coding_only -i $IN/$BASE.vcf -o $OUT/$BASE/$BASE.csv --cache --offline --refseq --format id --assembly GRCh37 --tab --ch…
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Hello:
When I run the Mastermind extension, it adds the comments to the output file in this way and does not add any mastermind information, but fills its columns with "-".
What is this error? How c…
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I have successfully annotated my vcf file using a local installation of variant effect predictor (VEP). However, the filtering doesn't work. E.g. the command
`filter_vep -i vep.test.vcf.gz -filter …
matmu updated
5 years ago
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Hi Brad,
just a quick question. Is there a reason you omitted some VEP annotation options during that step?
Wouldn't it be possible to just use the "--everything" option to maximize the annotations …
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So I tried posting this on the graphviz.org forum but to no avail.
The connection always timed out. So I will repost it here.
We have a graph (yes I know it is large) that is not too much bigger
…