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Here are general guidelines for analysis of data dependent acquisition acquired mass spectra (or, shotgun proteomics). @Ellior2 will be following these steps, Laura and Yaamini will be doing something…
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[PeptideShaker BugReport 1.13.6 log.txt](https://github.com/compomics/peptide-shaker/files/546157/PeptideShaker.BugReport.1.13.6.log.txt)
Hi, is this a memory issue as well? I was able to generate al…
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Both Dylan and a user (Benjamin Temperton) reported that they can't get spectral-counts to work. Here is the email from the mailing list
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I've just started playing with crux for some spectral co…
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Hello EDAM curators,
I would like to request a term for the
SEQUEST results file (.out) format
Cheers,
Gerhard Mayer
germa updated
8 years ago
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Hi, Peptide Shaker is crashing when I ask to use the PEP statistical analysis instead of FDR. I read a useful article on interpreting data and the PEP would be useful for me, since I just want to be s…
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Hi, I've been trying to merge over 100 BAM files.
First off, I aligned fastq files (both paired and singleton) using STAR to the genome, and generated my BAM files. The data was from a variety of dif…
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Hello,
I have tried running SearchGUI/MSGF+ using both the interface and the command line. During both methods, the database search freezes at the very beginning, still at "0% complete". I am encount…
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Windows 8. Did run into the following problem:
Could not load RT lookup dict from this location:
D:\projects\p2069\dataSearchResults\mgf\GRAY_HD\_ursgal_lookup.pkl
Indeed there is no pkl file at…
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I'm going to propose a new template for the Dockerfile, I'm planning to clean it and make it simple. Parts of the changes will include: removing the cmd commands from the header, adding the METADATA t…
prvst updated
8 years ago
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Hello,
I recently wanted to start using SearchGUI and Peptideshaker for Protein evaluation and made my first steps using X!Tandem and Amandy search engines on a few of my data files. After the sear…