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stsour authored Oct 2, 2024
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## Further analysis
The data files produced with this pipeline can be used for futher analysis of the substituted peptides. The results from running this pipeline as described in [Tsour *et al*](https://doi.org/10.1101/2024.08.26.609665) can be found in [decode output](https://drive.google.com/open?id=15YoTBTZh4MdtAqHbibkYieEqyLyFi5hb&usp=drive_fs) and used to generate the analyses and figures described in [decode_analysis](decode_analysis) and [decode_figures](decode_figures)
The data files produced with this pipeline can be used for futher analysis of the substituted peptides. The results from running this pipeline as described in [Tsour *et al*](https://doi.org/10.1101/2024.08.26.609665) can be found in [decode output](https://drive.google.com/open?id=15YoTBTZh4MdtAqHbibkYieEqyLyFi5hb&usp=drive_fs) and used to generate the analyses and figures described in [decode_analysis](decode_analysis) and [decode_figures](decode_figures) and [gnomAD_analysis](gnomAD_analysis)

Additional scripts for quantifying the non-modified peptides, proteins, and modified proteins from the MaxQuant search data are provided in ~/decode_pipeline/python_script/downstream_processing/. The output from these scripts used in generating publication figures are also provided in [decode output](https://drive.google.com/open?id=15YoTBTZh4MdtAqHbibkYieEqyLyFi5hb&usp=drive_fs)

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