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M1-M12-rtsSeeker.sh
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M1-M12-rtsSeeker.sh
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##hg38_HEK293_PSI_seq_rep1_cmc_M4_VS_M1_EndToEnd
nohup /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/rtsSeeker --fa /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa --fai /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa.fai --treat /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M4.STAR.Aligned.sortedByCoord.out.bam --input /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M1.STAR.Aligned.sortedByCoord.out.bam -p 1.5 -t 5 -r 0.05 -M 1 --gene /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/hg38.gencode.v30.tRNA.refseqNcRNA.geneAnno.bed12 -f 1 -m 0 -s -n -w 20 -o /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_PSI_seq_rep1_cmc_M4_VS_M1_EndToEnd/M4_M1_roc_all.bed 2>/public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_PSI_seq_rep1_cmc_M4_VS_M1_EndToEnd/M4_M1_roc_all_rtsSeeker.log
##hg38_HEK293_PSI_seq_rep2_cmc_M5_VS_M2_EndToEnd
nohup /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/rtsSeeker --fa /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa --fai /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa.fai --treat /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M5.STAR.Aligned.sortedByCoord.out.bam --input /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M2.STAR.Aligned.sortedByCoord.out.bam -p 1.5 -t 5 -r 0.05 -M 1 --gene /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/hg38.gencode.v30.tRNA.refseqNcRNA.geneAnno.bed12 -f 1 -m 0 -s -n -w 20 -o /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_PSI_seq_rep2_cmc_M5_VS_M2_EndToEnd/M5_M2_roc_all.bed 2>/public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_PSI_seq_rep2_cmc_M5_VS_M2_EndToEnd/M5_M2_roc_all_rtsSeeker.log
##hg38_HEK293_PSI_seq_rep3_cmc_M6_VS_M3_EndToEnd
nohup /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/rtsSeeker --fa /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa --fai /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa.fai --treat /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M6.STAR.Aligned.sortedByCoord.out.bam --input /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M3.STAR.Aligned.sortedByCoord.out.bam -p 1.5 -t 5 -r 0.05 -M 1 --gene /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/hg38.gencode.v30.tRNA.refseqNcRNA.geneAnno.bed12 -f 1 -m 0 -s -n -w 20 -o /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_PSI_seq_rep3_cmc_M6_VS_M3_EndToEnd/M6_M3_roc_all.bed 2>/public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_PSI_seq_rep3_cmc_M6_VS_M3_EndToEnd/M6_M3_roc_all_rtsSeeker.log
##hg38_HEK293_EDU_PSI_seq_V1_rep1_cmcAndTer_M7_VS_M1_EndToEnd
nohup /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/rtsSeeker --fa /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa --fai /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa.fai --treat /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M7.STAR.Aligned.sortedByCoord.out.bam --input /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M1.STAR.Aligned.sortedByCoord.out.bam -p 1.5 -t 5 -r 0.05 -M 1 --gene /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/hg38.gencode.v30.tRNA.refseqNcRNA.geneAnno.bed12 -f 1 -m 0 -s -n -w 20 -o /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_EDU_PSI_seq_V1_rep1_cmcAndTer_M7_VS_M1_EndToEnd/M7_M1_roc_all.bed 2>/public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_EDU_PSI_seq_V1_rep1_cmcAndTer_M7_VS_M1_EndToEnd/M7_M1_roc_all_rtsSeeker.log
##hg38_HEK293_EDU_PSI_seq_V1_rep2_cmcAndTer_M8_VS_M2_EndToEnd
nohup /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/rtsSeeker --fa /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa --fai /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa.fai --treat /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M8.STAR.Aligned.sortedByCoord.out.bam --input /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M2.STAR.Aligned.sortedByCoord.out.bam -p 1.5 -t 5 -r 0.05 -M 1 --gene /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/hg38.gencode.v30.tRNA.refseqNcRNA.geneAnno.bed12 -f 1 -m 0 -s -n -w 20 -o /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_EDU_PSI_seq_V1_rep2_cmcAndTer_M8_VS_M2_EndToEnd/M8_M2_roc_all.bed 2>/public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_EDU_PSI_seq_V1_rep2_cmcAndTer_M8_VS_M2_EndToEnd/M8_M2_roc_all_rtsSeeker.log
##hg38_HEK293_EDU_PSI_seq_V1_rep3_cmcAndTer_M9_VS_M3_EndToEnd
nohup /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/rtsSeeker --fa /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa --fai /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/snakemake/genome/hg38.fa.fai --treat /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M9.STAR.Aligned.sortedByCoord.out.bam --input /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/M3.STAR.Aligned.sortedByCoord.out.bam -p 1.5 -t 5 -r 0.05 -M 1 --gene /public/home/chenzr/software/qt_project/psiFinder_dev/psiFinder_v1/build/psiFinder/script/hg38.gencode.v30.tRNA.refseqNcRNA.geneAnno.bed12 -f 1 -m 0 -s -n -w 20 -o /public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_EDU_PSI_seq_V1_rep3_cmcAndTer_M9_VS_M3_EndToEnd/M9_M3_roc_all.bed 2>/public/home/chenzr/eduPsiSeq_v3_totalRNA/allProcessingData/STAR_EndToEnd/hg38_HEK293_EDU_PSI_seq_V1_rep3_cmcAndTer_M9_VS_M3_EndToEnd/M9_M3_roc_all_rtsSeeker.log