Changed directory name & added cecum qtl mapping loop

cecum_lipids_JAX_loop.sh

@@ -0,0 +1,12 @@
+cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts
+
+INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_cecum_lipids_qtl2_input.Rdata
+OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Cecum/lipids_norm_jax/
+SIZE=20
+
+# Set the maximum number in the loop to ceiling(MAXCOL/SIZE).
+for i in {1..113}
+do
+  qsub -v INDIR=${INPUT},OUTPREFIX=${OUTPUT},CHUNKSIZE=${SIZE},CHUNKNUM=${i} qtl2_scan_engine.sh
+  sleep 30s
+done

gather_qtl_output.sh

@@ -4,60 +4,60 @@ module load R/3.3.2
 
 # For each chromosome, harvest the maximum peak per analyte.
 
-cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts
+cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts
 
 # JAX normalized liver metabolites. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_jax/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_jax.Rout
 
 
 # JAX normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_jax_sex_gen.Rout
 
 
 # U. Wisc. normalized liver metabolites. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_uwisc.Rout
 
 
 # U. Wisc. normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_uwisc_sex_gen.Rout
 
 
 # JAX normalized liver lipids. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_jax/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_jax/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_lipids_jax.Rout
 
 
 # U. Wisc. normalized liver lipids. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_lipids_uwisc.Rout
 
 
 # JAX normalized plasma lipids. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_jax/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_jax/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_plasma_lipids_jax.Rout
 
 
 # U. Wisc. normalized plasma lipids. (NOTE: Place a / at the end of the paths)
-INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm
-FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/
+INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm
+FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/
 R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_plasma_lipids_uwisc.Rout
 

harvest_max_qtl.sh

@@ -4,56 +4,56 @@ module load R/3.3.2
 
 # For each chromosome, harvest the maximum peak per analyte.
 
-cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts
+cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts
 
 # Arguments.
 # INPUTFILE: full path to aggregated QTL LOD file (as *.rds).
 # OUTPUTPREFIX: full path to output file prefix. We append .csv and .rds to it.
 
 # JAX normalized liver metabolites. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_jax.Rout
 
 
 # JAX normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_jax_sex_gen.Rout
 
 
 # U. Wisc. normalized liver metabolites. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_uwisc.Rout
 
 
 # U. Wisc. normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_uwisc_sex_gen.Rout
 
 
 # JAX normalized liver lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_lipids_jax.Rout
 
 
 # U. Wisc. normalized liver lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_lipids_uwisc.Rout
 
 
 # JAX normalized plasma lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_plasma_lipids_jax.Rout
 
 
 # U. Wisc. normalized plasma lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_plasma_lipids_uwisc.Rout
 

harvest_thr_qtl.sh

@@ -5,54 +5,54 @@ module load R/3.3.2
 # For each chromosome, harvest the maximum peak above a given threshold for each analyte.
 # Run this AFTER the harvest_max_qtl.R script because it creates the aggregated QTL file.
 
-cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts
+cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts
 
 THR=6
 
 # JAX normalized liver metabolites. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_jax.Rout
 
 
 # JAX normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_jax_sex_gen.Rout
 
 
 # U. Wisc. normalized liver metabolites. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_uwisc.Rout
 
 
 # U. Wisc. normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_uwisc_sex_gen.Rout
 
 
 # JAX normalized liver lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_lipids_jax.Rout
 
 
 # U. Wisc. normalized liver lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_lipids_uwisc.Rout
 
 
 # JAX normalized plasma lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_plasma_lipids_jax.Rout
 
 
 # U. Wisc. normalized plasma lipids. (NOTE: Place a / at the end of the paths)
-INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds
-OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm
+INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds
+OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm
 R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_plasma_lipids_uwisc.Rout
 

liver_lipids_JAX_coef_assoc_loop.sh

@@ -1,13 +1,13 @@
-cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts
+cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts
 
 # The full path to the qtl2 data input file.
-DF=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_input.Rdata
+DF=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_input.Rdata
 # The full path to the QTL summary file.
-QF=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_qtl_summary_thresh_6.csv
+QF=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_qtl_summary_thresh_6.csv
 # Output directory for data.
-OD=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/
+OD=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/
 # Output directory for figures.
-FD=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/Liver/lipids_norm_jax/
+FD=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Liver/lipids_norm_jax/
 # Number of analytes to map in one chunk.
 SIZE=20