Activity
From 04/21/2019 to 05/20/2019
05/17/2019
- 11:08 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #82 (In Progress): Preliminary analysis of Proteome identification data
- 11:04 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #82 (Resolved): Preliminary analysis of Proteome identification data
- Differential abundance analysis of preliminary data, PCA and heatmap generation.
- 10:58 AM Infant stool metaproteome analysis Support #75 (Resolved): Taxonomic profiling using BLAST of identified proteins and peptides
05/16/2019
- 10:52 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #81 (Resolved): Full run on ilifu of RNA seq pipeline
- Full run started on ilifu.
Output dir:
/ceph/cbio/users/jambler/full_run
Execute script used:
/ceph/cbio/use...
05/15/2019
- 09:28 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #80 (Resolved): Renaming all files according to the experiments
- Files uploaded and renamed successfully.
05/14/2019
- 02:58 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #80 (In Progress): Renaming all files according to the experiments
- To make sure files are named correctly, a testing set was created where the files contained their original names to m...
- 12:18 PM Pathogen outbreak study - Pseudomonas single isolate WGS srst2 AMR and VFDB results transferred
- NB: there were some differences in results between Tychus and srst2 which seems to be due to different bowtie2 parame...
- 10:30 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #78 (Resolved): Proteomics raw data uploaded to Blackburn Lab researchdata
05/13/2019
- 10:58 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #80 (Resolved): Renaming all files according to the experiments
- Relebohile asked if the fastq files could be renamed according to the experimental conditions.
- 09:09 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #79 (Resolved): Uploading new data from BGI
- 09:09 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #79: Uploading new data from BGI
- Download completed, checksums passed.
Files moved to:
/ceph/cbio/users/jambler/Clean
checksum file for new sa... - 09:06 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #77 (Resolved): Testing pipeline on subset of data
- Strandedness is correct, pipeline ready for full dataset.
05/09/2019
- 04:29 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #79 (In Progress): Uploading new data from BGI
- Uploading the data directly to ilifu from the BGI ftp server.
- 04:28 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #79 (Resolved): Uploading new data from BGI
- New samples on the BGI server need to be uploaded. Login details contained in an email.
- 04:26 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #77 (In Progress): Testing pipeline on subset of data
- After dealing with some java issues, the pipeline ran through successfully.
The QC results look mostly good, just... - 03:12 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #78 (Resolved): Proteomics raw data uploaded to Blackburn Lab researchdata
- Files uploaded to:
/mnt/researchdata/BLACKBURNLAB/2019/Collaborations/Thys/keloid
05/03/2019
- 09:55 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #77 (Resolved): Testing pipeline on subset of data
- We are going to test the pipeline on a subset of the samples to make sure that the pipeline is functioning correctly....
- 09:40 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #73 (Closed): Initial meeting
- 09:39 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #74 (Resolved): Uploading of data
- All samples uploaded
1 sample failed checksum
Clean/GSH-FKN-002/CL100118345_L2_WHHUMyhwEACYRAA-588_2.fq.gz
re-upl...
05/02/2019
- 07:32 AM Pathogen outbreak study - Pseudomonas single isolate WGS Feedback on pipeline results from Nicol group
- We have been analysing the data you sent us and its looking really good. We are trying to do some additional analyses...
04/29/2019
- 06:01 PM HIV latency transcriptomics of resting CD4+ T cells Results from run 1 sent to Walter - QC issues detected
- The multiqc report highlighted potential issues with sample and/or library prep. A large proportion of reads were < 1...
- 09:44 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #74: Uploading of data
- Started upload of the data to Ilifu.
Location:
/ceph/cbio/users/jambler
04/26/2019
- 10:52 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #74: Uploading of data
- Ok the private folder is there on Ilifu now.
04/25/2019
- 05:28 PM Infant stool metaproteome analysis Support #75 (Resolved): Taxonomic profiling using BLAST of identified proteins and peptides
- BLAST analysis of infant stool peptides and proteins, using the CHPC peptide BLAST pipeline.
- 04:57 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #73 (Resolved): Initial meeting
- Relebohile outlined the study design, and elaborated on the research questions they are seeking to answer.
We outlin... - 04:45 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #74: Uploading of data
I've requested to setup a POSIX group for this project (`cbio-002`) on Ilifu.
Jon for now you can move the data ...- 04:39 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #74 (Resolved): Uploading of data
- Getting data onto Ilifu
04/24/2019
- Support request form
- 11:42 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #73 (Closed): Initial meeting
- A meeting has been arranged for the 25/04/19 at 15:00 to discuss the project.
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