question about script 'RAW_search_overlap.slurm'

[dengyuan7]

Dear Lex,

I would like to use the scripts from 'S23_S25_MHC_I_target_sequence_generation_and_read_count' to estimate the copy number of avian MHC genes, but I am not sure what the 'QUERY' and 'TARGET' are in the RAW_search_overlap.slurm .

for QUERY in $(cat Query_names)

for TARGET in $(cat ~/MCMC_METODE/QUERIES/Targets) 
do

##SUM OF UNIQUE READS FOR ${TARGET} FROM OWN SPECIES + ALL ENSEMBLE SPECIES (-COD)
cat ${TARGET}_Danrer_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Gasacu_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Orylat_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Orenil_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Takrub_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Tetnig_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Poefor_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Xipmac_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_Astmex_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all
cat ${TARGET}_${FISH}_all >> Own_and_ENSEMBLE_nocod_${TARGET}_uncut_all

I suppose Query_names means the consensus sequences of all 66 fishes. But I have no idea about TARGET and how to get the files like ${TARGET}_Danrer_all and ${TARGET}_fish_*_all.

Any help much appreciated.
Yuan