Changlin Ke

Changlin Ke

Your biography for the left-hand sidebar

Work list of ongoing and completed projects

Date:

Work List

Changlin Ke

Modification

  • To add email notification function to qsub cmd: -M changlin@macrogen-europe.com
  • “/mnt/ruby/Tools/WES_Analysis/DATA_TRANSFER/hddlist_build.sh” line 46, chir changed to chdir

Development

Auto weekly report tool

a simple script to generate your weekly work report 😀, it only needs your name and a location to save output excel file. After getting the file, copy paste the content to the template as you like.

There is possibility that unfinished orders on Friday would be lost/missed if they are updated to complete after submitting weekly report.

Use bi2 account, and conda activate celescope (a lot of packages are pre-installed, I just use this env for convenience)

Run: python /mnt/ruby/Users/changlin/WeeklyReport_auto/Create_WeeklyReport.py [ANALYZER] -o [PATH_FOLDER_OUTPUT] -f [PATH_WORKSHEET] -d [INPUT_DATE_PERIOD] Example: python /mnt/ruby/Users/changlin/WeeklyReport_auto/Create_WeeklyReport.py Jongbum /mnt/ruby/Users/changlin/WeeklyReport_auto/

Macrogen EU Singleron single-cell data Analysis Pipeline (MASP)

Currently covered features: scRNA-seq data preprocessing based on Celescope

To do:

  1. Data and analysis (intermediatory) result deliverables packing based on customer needs.
  2. Adapt to snakemake

auto data upload script

WES: Upload data from latest report folder to customer’s cloud (dropbox), pre-configure cloud service connection before running!

/mnt/ruby/Tools/cke_script/LinkAndUppdate.sh [EN0000xxxx] [upload_batch]

Bug record & question

  1. error message no JSON object could be decoded:

    check json file and delete existing file if it’s empty.

  2. why is the file in “/mnt/ruby/Analysis/BI/WholeGenomeReSeq/” sometimes incomplete. For instance, no sqs file in merge_analysis of some sample?

Todo List

  1. Fix pcname parameter of hdd1.list hdd copy script generated by /mnt/ruby/Tools/WES_Analysis/DATA_TRANSFER/hddlist_build.sh
  2. complete /mnt/ruby/Tools/cke_script/awesome_qstat.py
    • qstat monitor and email automatically when monitored jobs are done
  3. make docker images

Work of others

  • Simone: a small script to communicate with lab team, when we have a low mean depth of target region scenario. Under maintainance
    • USAGE: BTS_mean_depth_target_region.py [ordernumber_excelstat.csv] [contracted Depth] [contracted throughput]
    • The csv file can be downloaded from BTS monitoring page generated with /ruby/Tools/BTS_monitoring_pipeline/makeExomeChart_sales.py [OrderNum] [appcode EXO|TAG] (by Jongbum).
    • The output is an excel file with all the bad quality data. In a scenario like Nima’s : two different contracted throughputs matched with two different depth coverage, we can run it two times and then merge the two different files with another script:"/mnt/ruby/Tools/BTS_monitoring_pipeline/merge_excel_files.py".

Career

Strong interest / higher chance:

  1. PhD Candidate Rheumatology Data Science at LUMC 1.22/2.12 https://www.lumc.nl/en/over-het-lumc/werken-bij/vacancies/b.23.pv.el.03-phd-candidate-rheumatology-data-science/ https://lumc.recruitee.com/l/en/o/b23pvel03-phd-candidates-rheumatology-data-science/c/new#apply
  2. PhD Candidate Clinical Data Science at Netherlands Comprehensive Cancer Organisation (IKNL) and Amsterdam UMC 1.15/1.16 https://vacatures.iknl.nl/vacaturebeschrijving-2/phd-candidate-clinical-data-science
  3. PhD 2x - Comorbidities of serious mental illness 2.5 https://werkenbij.amsterdamumc.org/nl/vacatures/research/phd-2x—comorbidities-of-serious-mental-illness?utm_source=Indeed&utm_medium=organic&utm_campaign=Indeed
  4. PHD-candidate in genetics at BPRC(Ben Becker Internationaal Transportbedrijf) and Utrecht University 3.15 https://debanensite.nl/vacature/phd-candidate-in-genetics-rijswijk/c36bf771-cb58-410a-ae15-5a2a3dab6528
  5. Longtrec project 1.21
  6. PhD position in systems biology at RUG https://www.academictransfer.com/en/322448/post-doc-phd-position-in-systems-biology/apply/#apply

Less likely

  1. VU ctg lab: incoming jobs
  2. PhD Statistical and health-economic modeling to optimize cancer prevention at Amsterdam UMC, 2.1 https://werkenbij.amsterdamumc.org/nl/vacatures/research/phd-statistical-and-health-economic-modeling-to-optimize-cancer-prevention

motivation

Story connecting achivements:

needed future environment to communicate with great ppl A struggle to preserve, set free a suffering humanity.