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qc.phyllo.simple.sh
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#!/bin/bash
#$ -V
#$ -cwd
#$ -S /bin/bash
#$ -N QC
#$ -o $JOB_NAME.o$JOB_ID
#$ -e $JOB_NAME.e$JOB_ID
#$ -q R2D2
#$ -pe fill 5
#$ -P communitycluster
cd /lustre/scratch/daray/ray_phyllo/HiSeq/Sample_46394
zcat 46394_R1.fastq.gz | /lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_filter -Q33 -q20 -p 50 -o 46394_R1_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_quality_stats \
-Q33 \
-o 46394_R1_QC.stats \
-i 46394_R1_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_nucleotide_distribution_graph.sh \
-i 46394_R1_QC.stats \
-o 46394_R1_QC_NUC.png \
-t 46394_R1_QC
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_boxplot_graph.sh \
-i 46394_R1_QC.stats \
-o 46394_R1_QC_BOX.png \
-t 46394_R1_QC
zcat 46394_R2.fastq.gz | /lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_filter -Q33 -q20 -p 50 -o 46394_R2_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_quality_stats \
-Q33 \
-o 46394_R2_QC.stats \
-i 46394_R2_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_nucleotide_distribution_graph.sh \
-i 46394_R2_QC.stats \
-o 46394_R2_QC_NUC.png \
-t 46394_R2_QC
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_boxplot_graph.sh \
-i 46394_R2_QC.stats \
-o 46394_R2_QC_BOX.png \
-t 46394_R2_QC
cd /lustre/scratch/daray/ray_phyllo/HiSeq/Sample_46395
zcat 46395_R1.fastq.gz | /lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_filter -Q33 -q20 -p 50 -o 46395_R1_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_quality_stats \
-Q33 \
-o 46395_R1_QC.stats \
-i 46395_R1_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_nucleotide_distribution_graph.sh \
-i 46395_R1_QC.stats \
-o 46395_R1_QC_NUC.png \
-t 46395_R1_QC
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_boxplot_graph.sh \
-i 46395_R1_QC.stats \
-o 46395_R1_QC_BOX.png \
-t 46395_R1_QC
zcat 46395_R2.fastq.gz | /lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_filter -Q33 -q20 -p 50 -o 46395_R2_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_quality_stats \
-Q33 \
-o 46395_R2_QC.stats \
-i 46395_R2_QC.fastq
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastx_nucleotide_distribution_graph.sh \
-i 46395_R2_QC.stats \
-o 46395_R2_QC_NUC.png \
-t 46395_R2_QC
/lustre/work/apps/fastx_toolkit-0.0.14/bin/fastq_quality_boxplot_graph.sh \
-i 46395_R2_QC.stats \
-o 46395_R2_QC_BOX.png \
-t 46395_R2_QC