Please refer here for details. We would need the .db file and .ReadsPerSample.log file to normalize reads
#!/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
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)]
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