20210310 - LSCI6306 tutorial meeting note

Time: 2021/03/10 4pm
Participant: Andy, Claire, Delbert
Venue:

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Tutorial Zoom link

https://cuhk.zoom.us/j/96572218205?pwd=RlZtQld5Y1JqWU42a3FNK0t3OWVTUT09

Program flow

• Brief intro of the tutorial(Claire)
• Bionano Access account settings (Delbert)
• Assembly & scaffolding (Delbert)
• Alignment & SV detection (Claire)
• Q&A, chat box & session (Andy)
• (section distribution with internet connection stability from local/mainland considered)

To-dos

• Enable computing components (Claire)
• Test functionalities (all)
• Prep slides & work for teaching sessions (Claire & Delbert)

Post-class matters

• handout for installation (Claire)
• announcement for server closing time

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Material preparation

FASTA reference

• https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
• ftp://ftp.ensemblgenomes.org/pub/plants/release-50/fasta/arabidopsis_thaliana/dna/
• Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
• File size: 35Mb

OM datasets

• Dropbox link of files below for back up:

  • https://www.dropbox.com/sh/8rm07255c33d2xn/AAC0Kqhxy86huajBLMsLzyEEa?dl=0

• try 232 & 075892

• sail_232_bng_contigs.cmap

  • https://submit.ncbi.nlm.nih.gov/ft/byid/6aogclxy/sail_232_bng_contigs.cmap
  • SAMN07141933-sail_232_bng_contigs.cmap
  • c126b8ca9473a04b9f4d96eb7200dedd

• salk_059379_bng_.cmap

  • https://submit.ncbi.nlm.nih.gov/ft/byid/sivbjy1c/salk_059379_bng_.cmap
  • SAMN07141931-salk_059379_bng_.cmap
  • f238bdd8c159d91db4ed2178dfc95b4c

• salk_075892.cmap

  • https://submit.ncbi.nlm.nih.gov/ft/byid/9dgny8fd/salk_075892.cmap
  • SAMN07141932-salk_075892.cmap
  • 70508af153cde411a730c5de62495c86

• wiscseq_dslox449d11_bng_contigs.cmap

  • https://submit.ncbi.nlm.nih.gov/ft/byid/irzfa1ct/wiscseq_dslox449d11_bng_contigs.cmap
  • SAMN07141934-wiscseq_dslox449d11_bng_contigs.cmap
  • 4ec16402c67cc2b086103c55cc3a4878

• sail_232_merged_molecules.bnx

  • https://submit.ncbi.nlm.nih.gov/ft/byid/ftujde8s/sail_232_merged_molecules.bnx
  • SAMN07141933-sail_232_merged_molecules.bnx
  • 1d7e79396b168d98181b9667b18dbb2f

• salk_059379_merged_molecules.bnx

  • https://submit.ncbi.nlm.nih.gov/ft/byid/waf3nzeh/salk_059379_merged_molecules.bnx
  • SAMN07141931-salk_059379_merged_molecules.bnx
  • 457b42359e6830c2c6c575b349b1b48c

• salk_075892_merged_molecules.bnx

  • https://submit.ncbi.nlm.nih.gov/ft/byid/ipw0xhyj/salk_075892_merged_molecules.bnx
  • SAMN07141932-salk_075892_merged_molecules.bnx
  • 55be9136775f552b16282d32a2c5969d

• wiscseq_dslox449d11_merged_molecules.bnx

  • https://submit.ncbi.nlm.nih.gov/ft/byid/okq4d1tr/wiscseq_dslox449d11_merged_molecules.bnx
  • SAMN07141934-wiscseq_dslox449d11_merged_molecules.bnx
  • cdb041d7c8ba46fd39d4b58caad6930b

• kbs-mac-74_bng_contigs2017.cmap

  • https://submit.ncbi.nlm.nih.gov/ft/byid/w4jceved/kbs-mac-74_bng_contigs2017.cmap
  • SAMN07224378-kbs-mac-74_bng_contigs2017.cmap
  • fe82cafbdcff445dfc8c515b7a4574e2

Bionano Access

URL

137.189.43.52:3005

User accounts

user001 lsci001
user002 lsci002
user003 lsci003
user004 lsci004
user005 lsci005
user006 lsci006
user007 lsci007
user008 lsci008

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References

Installation

• Bionano Solve (computing components)
  https://bionanogenomics.com/wp-content/uploads/2017/10/30182-Bionano-Tools-Installation-Guide.pdf
• Bionano Access (web portal)
  https://bionanogenomics.com/wp-content/uploads/2018/04/30170-Bionano-Access-Installation-Guide.pdf