Tuesday, February 7, 2017

fastqc command

/mnt/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /mnt/BioAdHoc/Users/zfu/packages/FastQC/Configuration/contaminants_LJI.txt -o /mnt/overflow/NGSAnalyses/QC/QC_Validation/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502 -t 2 /mnt/overflow/BioAdHoc/Users/zfu/2017_Trimming/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502/BeforeTrimming.28_C1_038_C50_N705S502_R1.fastq.gz

/mnt/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /mnt/BioAdHoc/Users/zfu/packages/FastQC/Configuration/contaminants_LJI.txt --casava -o /mnt/overflow/BioAdHoc/Users/zfu/2017_Trimming/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/output/28_C1_038_C50_N705S502 -t 2 /mnt/overflow/BioAdHoc/Users/zfu/2017_Trimming/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502/28_C1_038_C50_N705S502_GGACTCCT-CTCTCTAT_L002_R2_001.fastq.gz

/mnt/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /mnt/BioAdHoc/Users/zfu/packages/FastQC/Configuration/contaminants_LJI.txt -o /mnt/overflow/NGSAnalyses/QC/QC_Validation/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502 -t 2 /mnt/overflow/BioAdHoc/Users/zfu/2017_Trimming/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502/BeforeTrimming.28_C1_038_C50_N705S502_R2.fastq.gz


/mnt/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /mnt/BioAdHoc/Users/zfu/packages/FastQC/Configuration/contaminants_LJI.txt -o /mnt/overflow/NGSAnalyses/QC/QC_Validation/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502 -t 2 /mnt/overflow/BioAdHoc/Users/zfu/2017_Trimming/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/trimmed/28_C1_038_C50_N705S502/AfterTrimming.28_C1_038_C50_N705S502_R1.fastq.gz

/mnt/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /mnt/BioAdHoc/Users/zfu/packages/FastQC/Configuration/contaminants_LJI.txt -o /mnt/overflow/NGSAnalyses/QC/QC_Validation/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/28_C1_038_C50_N705S502 -t 2 /mnt/overflow/BioAdHoc/Users/zfu/2017_Trimming/160804_D00361_0380_AHK3VCBCXX_8_4_16_GrSe60B_AaMi_150x150/trimmed/28_C1_038_C50_N705S502/AfterTrimming.28_C1_038_C50_N705S502_R2.fastq.gz
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