20210310 - LSCI6306 tutorial meeting note
==

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

---

## 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

---

## 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

---

## 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