# cpang22 notes

HLA/MHC stuff

https://docs.google.com/presentation/d/1nCcxsb1GACaNMuMGiOLspY2WJDO-aMPEDtLsdnA67Pw/edit?usp=drivesdk

https://docs.google.com/presentation/d/1N7DrtIpMLI7WQ8b0DaqgcZD0mzdehpg6j2QPJQgO5MQ/edit?usp=drivesdk

HPRC paper draft figures
https://docs.google.com/presentation/d/1Za8EhZJ3RTNN3ZZZsWn9_nbFrdFC5tV0leo6-DAzaC4/edit#slide=id.p

HPRC supplement draft
https://docs.google.com/document/d/1R5_6lbMpGmh8XxRqmaWx-JMNyxOD1WnokNSnlHyxvms/edit#

building the HPRC graphs
https://docs.google.com/presentation/d/1qDSHpi1i2esmnIuiBA0g5EOGzvq8jUnkIw1yFFrp4hw/edit?usp=sharing

## acrocentric community stuff

https://docs.google.com/presentation/d/11Qy-OBPqSRSIynIyy5q4rHWrw1DsiDAJvYxmKGSItNk/edit?usp=drivesdk

## GWAS

catalog of GWAS results (for group projects)
https://docs.google.com/spreadsheets/d/1FNfQ0Azlex5V8V0Zu5OnODMLvKoPyQqE2NzZhs2BtDA/edit#gid=666027808

paper describing this catalog
https://doi.org/10.1016/j.ajhg.2021.03.009

Human pangenome graphs (90 haplotypes)

n=1 # Specify the chromosome you want (1, 2, ..., X, Y)
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/scratch/2021_11_16_pggb_wgg.88/chroms/chr$n.pan.fa.a2fb268.4030258.6a1ecc2.smooth.gfa.gz

Browsable link
https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/scratch/2021_11_16_pggb_wgg.88/

Yeast short reads data
fasterq-dump --split-files ERR1309471 #CBS457 #1. Wine/European (01.W)
fasterq-dump --split-files ERR1309488 #EXF-7197 #4. Mediterranean oak (04.M)

fasterq-dump --split-files ERR1309190 #UCD_05-780 #M3. Mosaic (M3.M)
fasterq-dump --split-files ERR1309331 #N37-1A #M3. Mosaic (M3.M)

fasterq-dump --split-files ERR1308911 #CLIB415 #26. Asian fermentation (26.A)
fasterq-dump --split-files ERR1309400 #K14 #25. Sake (25.S)