running_JUM.sh

#Assuming we have our SAM, BAM ready
#check the read length from fastqc of trimmed files.

bash ../JUM_2.0.2/JUM_A.sh --Folder ../JUM_2.0.2 --JuncThreshold 3 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 3 --Readlength 140 --Thread 2 --Condition1SampleName col_1,col_2,col_3 --Condition2SampleName dex_1,dex_2,dex_3

echo "DONE"

cd JUM_diff

Rscript /user/home/JUM_2.0.2/R_script_JUM.R experiment_design.txt > outputFile.Rout 2> errorFile.Rout

bash ../JUM_2.0.2/JUM_B.sh --Folder ../JUM_2.0.2 --Test pvalue --Cutoff 0.05 --TotalFileNum 6 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName col_1,col_2,col_3 --Condition2SampleName dex_1,dex_2,dex_3

#it will create a new folder

#now taking qvalue into account:

bash ../JUM_2.0.2/JUM_B.sh --Folder ../JUM_2.0.2 --Test adjusted_pvalue --Cutoff 0.05 --TotalFileNum 6 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName col_1,col_2,col_3 --Condition2SampleName dex_1,dex_2,dex_3

#it will also create a new folder

cd FINAL_JUM_OUTPUT_pvalue_0.05


bash ../JUM_2.0.2/JUM_C.sh --Folder ../JUM_2.0.2 --Test pvalue --Cutoff 0.05 --TotalCondition1FileNum 3 --TotalCondition2FileNum 3 --REF TAIR10.1_genePred_bygff.txt

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