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Example: https://mila.quebec/en/publications/
It would be nice to reuse the same code as in the Mila website. Not sure if that's 'easily' possible via RTD
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**Describe the bug**
Hello,
I'm trying to generate a spectral library from Thermo DDA runs. I'm running FragPipe in headless mode in Linux with a workflow copied from the GUI to include spectral l…
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Hello,
when running FragPipe in headless mode (analyzing a TMT experiment), I get weird TMT channel names. I put an example here: https://oc.embl.de/index.php/s/9iEiAtMw6j0hSMK
In the annotatio…
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Hi,
I tried processing Thermo raw data (DDA runs) in Frappe 19. The error I get is:
java.lang.IllegalArgumentException: No matching mzml/mgf file for QEP2_GVAI_10_12-11-01563_10_1_230316_uncalibrate…
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Hello,
I'm having trouble understanding the results from a SILAC run.
In the main proteome file, I can see the labelled proteins and how many labels there were, but i
[log_2022-05-12_16-05-47.txt…
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search stopped with the following error:
Process 'PhilosopherFilter' finished, exit code: 2
Process returned non-zero exit code, stopping
search was LFQ-MBR with two additional modifications. p…
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Dear developers
i have issues during philosopher pipeline running
here is the log
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INFO[12:12:33] Executing report on set42
INFO[12:12:43] Creating reports …
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Dear FragPipe team.
I am re-running an analysis of two TMT11plex sets on FragPipe, same parameter as before, just with a custom made FASTA, decoys were added using FragPipe.
MSFragger, Percolator a…
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Why does the fasta header of the database affect the results?
I built the database from the metagenome, so the fasta header of the database does not follow the standard form of NCBI or uniprot.
Ho…
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I have not been able to run the Linus version of Dia-NN and so have tried running on Linux using Wine. Unfortunately the software exits as soon as the run is implemented. A typical log output:
dian…