Alien (2NS) Predict Based on GBS data

(1) Run TASSEL GBSv2 pipeline to get the database populated.

Please refer here for details. We would need the .db file and .ReadsPerSample.log file to normalize reads

(2) Extract tag by taxa file for selected tags

#!/bin/bash
prj_name='ventri2ns_sub483'
prj_dir='~/ventri2ns/data/gbs/gbs_KS_to2A2N_v3_sub483'; 
cd $prj_dir
tasselPath="~/src/tassel-5-modif/run_pipeline.pl" 
## needs to replace the sTASSEL.jar file with modified .jar (f66b3f4d37aa51e401f44b9eaacad45c) to use GetSelTagTaxaDistFromDBPlugin
sqlite_db='ventri2ns.db'
seltags='~/ventri2ns/zz_results/rebuild.2ns.based.on.tassel/archive/171130.tags.cmb.txt'

## GetSelTagTaxaDistFromDBPlugin extract tags and their taxa distribution
$tasselPath -Xms10G -Xmx40G -fork1 -GetSelTagTaxaDistFromDBPlugin \
    -db $sqlite_db\
    -o ${prj_name}_SelTagTaxaDistOutput.txt \
    -tg $seltags\
    -endPlugin -runfork1 > z_${prj_name}_GetSelTagTaxaDistFromDBPlugin.out \
    2> z_${prj_name}_GetSelTagTaxaDistFromDBPlugin.err

(3) Import the geno_predict function and predict the results

library(data.table)
source("~/Alien_Predict/scripts/functions/fn01_geno_predict.R")

my.results = geno_predict(atag.file = "~/Alien_Predict/data/2NS/KSU//tags.alien.txt", 
    wtag.file = "~/Alien_Predict/data/2NS/KSU//tags.wheat.txt", 
    tbt = "~/ventri2ns/data/gbs/gbs_KS_to2A2N_v3_sub483/ventri2ns_sub483_SelTagTaxaDistOutput.txt", 
    log = "~/ventri2ns/data/gbs/gbs_KS_to2A2N_v3_sub483/170708.orig28_minus_1_ReadsPerSample.log")
my.results[!is.na(adjusted.predict), plot(norm1, norm2, col = COL, 
    xlab = "Normalized alien tag count", ylab = "Normalized wheat tag count", 
    font.lab = 2)]

If you use this pipeline, please cite a paper:

Gao L, Koo D-H, Juliana P, et al (2020) The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding. Theoretical and Applied Genetics https://doi.org/10.1007/s00122-020-03712-y