Redmine

07/02/2019

11:36 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 3.00 hours (Support #90 (Resolved): QC of aligned reads)

Jon Ambler

11:28 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 6.00 hours (Support #92 (Resolved): Differential expression analysis)

Jon Ambler

09:21 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 2.00 hours (Support #86 (Resolved): Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu)

Methods summary presentation created and sent to Relebohile Thys Potgieter

09:21 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 2.00 hours (Support #86 (Resolved): Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu)

Data analyzed, experimental design file created for cells and tissues separately. Thys Potgieter

09:19 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 6.00 hours (Support #86 (Resolved): Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu)

Bug fixes and unit tests for mqmetaproteomics pipeline Thys Potgieter

09:18 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 6.00 hours (Support #86 (Resolved): Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu)

Quality control - samples less than 1 percent assigned spectra excluded. normalization and imputation methods tested. Thys Potgieter

09:16 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 2.00 hours (Support #85 (Resolved): MaxQuant run of raw proteomics data)

MaxQuant run restarted, experiment names added Thys Potgieter

06/24/2019

04:42 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 5.00 hours (Support #92 (Resolved): Differential expression analysis)

Creating the design_formula file needed to create DESeqDataSet Jon Ambler

04:40 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 6.00 hours (Support #92 (Resolved): Differential expression analysis)

Sample gene counts need to be merged Jon Ambler

06/19/2019

12:53 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 1.00 hour (Support #81 (Resolved): Full run on ilifu of RNA seq pipeline)

Jon Ambler

06/18/2019

02:27 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 2.00 hours (Support #90 (Resolved): QC of aligned reads)

Initial overview Jon Ambler

11:32 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 8.00 hours (Support #81 (Resolved): Full run on ilifu of RNA seq pipeline)

Multiple parameters had to be changed with the genebody_coverage process taking a long time to run. Jon Ambler