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work_log_TGCT
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perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 1
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 2
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 3
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 4
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 5
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 6
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 7
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 8
perl misplice.pl --rdir /gscmnt/gc2517/dinglab/scao/scm/TGCT --bed /gscmnt/gc2518/dinglab/scao/home/tools/MiSplice_CPTAC/resource/GRCh38/E95_bed_v3.tsv --ref /gscmnt/gc2518/dinglab/scao/tools/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa --maf /gscmnt/gc2686/rna_editing/TCGA-TGCT/synapse/somaticwrapper_tcga_tgct_270samples.maf --bamlist /gscmnt/gc2517/dinglab/scao/scm/TGCT/rna.bamlist.tsv --n 100 --q research-hpc --step 9