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Demux script for C4W17ACXX
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#!/bin/bash | |
NAME="C4W17ACXX" | |
EMAIL='lg1883@nyu.edu' | |
FLOWCELL_PATH="/scratch/gencore/hiseq-700911/140710_SN911_0221_AC4W17ACXX" | |
OUTPUT_PATH="/scratch/gencore/manual/140710_SN911_0221_AC4W17ACXX" | |
CONFIGURE_BCL2FASTQ="\ | |
--fastq-cluster-count 0 \ | |
--use-bases-mask \"Y*,I6n\" \ | |
--no-eamss \ | |
--mismatches 1" | |
SAMPLESHEET_CONTENT="\ | |
C4W17ACXX,2,Undetermined,,Undetermined,,N,,lhw235@nyu.edu,Undetermined | |
C4W17ACXX,2,LW175,,GTCCGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW176,,GTGAAA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW177,,GTGGCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW178,,GTTTCG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW179,,CGTACG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW180,,GAGTGG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW181,,GGTAGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW182,,ATCACG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW183,,CGATGT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW184,,TTAGGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW185,,TGACCA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW186,,ACAGTG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW187,,GCCAAT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW188,,CAGATC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW189,,ACTTGA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW190,,GATCAG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW191,,TAGCTT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW192,,GGCTAC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW193,,CTTGTA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,2,LW194,,AGTCAA,,N,,lhw235@nyu.edu,Condensins | |
C4W17ACXX,2,LW195,,AGTTCC,,N,,lhw235@nyu.edu,Condensins | |
C4W17ACXX,2,LW196,,ATGTCA,,N,,lhw235@nyu.edu,Seaurchin | |
C4W17ACXX,3,Undetermined,,Undetermined,,N,,lhw235@nyu.edu,Undetermined | |
C4W17ACXX,3,LW197,,CCGTCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW198,,GTAGAG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW199,,GTCCGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW200,,GTGAAA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW201,,GTGGCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW202,,GTTTCG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW203,,CGTACG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW204,,GAGTGG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW205,,GGTAGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW206,,ATCACG,,N,,lhw235@nyu.edu,Seaurchin | |
C4W17ACXX,3,LW207,,CGATGT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW208,,TTAGGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW209,,TGACCA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW210,,ACAGTG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW211,,GCCAAT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW212,,CAGATC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW213,,ACTTGA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW214,,GATCAG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW215,,TAGCTT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW216,,GGCTAC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW217,,CTTGTA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW218,,AGTCAA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW219,,AGTTCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,3,LW220,,ATGTCA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,Undetermined,,Undetermined,,N,,lhw235@nyu.edu,Undetermined | |
C4W17ACXX,4,LW221,,CCGTCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW222,,GTAGAG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW223,,GTCCGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW224,,GTGAAA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW225,,GTGGCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW226,,GTTTCG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW227,,CGTACG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW228,,GAGTGG,,N,,lhw235@nyu.edu,Seaurchin | |
C4W17ACXX,4,LW229,,GGTAGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW230,,ATCACG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW231,,CGATGT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW232,,TTAGGC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW233,,TGACCA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW234,,ACAGTG,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW235,,GCCAAT,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW236,,CAGATC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW237,,ACTTGA,,N,,lhw235@nyu.edu,Condensins | |
C4W17ACXX,4,LW238,,GATCAG,,N,,lhw235@nyu.edu,Condensins | |
C4W17ACXX,4,LW239,,TAGCTT,,N,,lhw235@nyu.edu,Condensins | |
C4W17ACXX,4,LW240,,GGCTAC,,N,,lhw235@nyu.edu,Condensins | |
C4W17ACXX,4,LW241,,CTTGTA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW242,,AGTCAA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW243,,AGTTCC,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,4,LW244,,ATGTCA,,N,,lhw235@nyu.edu,DosageComp | |
C4W17ACXX,5,Undetermined,,Undetermined,,N,,nz375@nyu.edu,Undetermined | |
C4W17ACXX,5,SoilN_1,,CGATGT,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,5,SoilF_1,,TGACCA,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,5,DGY952_1,,ACAGTG,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,5,DGY955_1,,GCCAAT,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,5,SoilF2Pool_1,,CAGATC,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,Undetermined,,Undetermined,,N,,nz375@nyu.edu,Undetermined | |
C4W17ACXX,6,DGY1162_1,,CTTGTA,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,DGY1163_1,,ATCACG,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,DGY1166_1,,TTAGGC,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,DGY1167_1,,ACTTGA,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,DGY1179_1,,GATCAG,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,DGY1180_1,,TAGCTT,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,6,DGY1181_1,,GGCTAC,,N,,nz375@nyu.edu,SoilStrains | |
C4W17ACXX,7,Undetermined,,Undetermined,,N,,sv49@nyu.edu,Undetermined | |
C4W17ACXX,7,SV16,,ACAGTG,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,7,SV17,,CAGATC,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,7,SV18,,GCCAAT,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,7,SV19,,TGACCA,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,7,SV20,,CGATGT,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,8,Undetermined,,Undetermined,,N,,sv49@nyu.edu,Undetermined | |
C4W17ACXX,8,SV21,,TGACCA,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,8,SV22,,GCCAAT,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,8,SV23,,ACAGTG,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,8,SV24,,CGATGT,,N,,sv49@nyu.edu,NILProgramming | |
C4W17ACXX,8,SV25,,CAGATC,,N,,sv49@nyu.edu,NILProgramming | |
" | |
CORES=12 | |
BCL_TO_FASTQ_CMD="/share/apps/bcl2fastq/1.8.4/gnu/bin/configureBclToFastq.pl" | |
SAMPLE_SHEET_HEAD="FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject" | |
BCL2FASTQ_PATH="$OUTPUT_PATH/bcl2fastq" | |
FASTQC_PATH="$OUTPUT_PATH/fastqc" | |
PBS_PATH="$OUTPUT_PATH/bcl2fastq.pbs" | |
SAMPLESHEET_PATH="$OUTPUT_PATH/SampleSheet.csv" | |
PBS_HEAD="#!/bin/sh | |
#PBS -V | |
#PBS -l nodes=1:ppn=$CORES,walltime=48:00:00 | |
#PBS -M $EMAIL | |
#PBS -m abe | |
#PBS -q s48 | |
#PBS -l mem=16GB" | |
make_bcl2fastq_pbs() { | |
echo -e "\ | |
$PBS_HEAD | |
$BCL_TO_FASTQ_CMD \ | |
--input-dir $FLOWCELL_PATH/Data/Intensities/BaseCalls \ | |
--output-dir $BCL2FASTQ_PATH/Unaligned \ | |
--sample-sheet $SAMPLESHEET_PATH \ | |
$CONFIGURE_BCL2FASTQ; | |
cd $BCL2FASTQ_PATH/Unaligned; | |
make -j$CORES; | |
result=\$?; | |
# load the fastqc module | |
module load fastqc | |
# run fastqc on each of the fastq files | |
for fastq in $BCL2FASTQ_PATH/Unaligned/Project_*/*/*.fastq.gz | |
do | |
fastqc --noextract --threads $CORES --outdir $FASTQC_PATH \$fastq; | |
done | |
# make a tarball out of all fastqc reports | |
cd $OUTPUT_PATH && tar -cjf $NAME.tar.bz2 fastqc | |
exit \$result;" > $PBS_PATH | |
} | |
make_sample_sheet(){ | |
echo -e "$SAMPLE_SHEET_HEAD\n$SAMPLESHEET_CONTENT" > $SAMPLESHEET_PATH | |
} | |
make_output_directories(){ | |
rm -rf "$OUTPUT_PATH" | |
mkdir -p "$OUTPUT_PATH" | |
mkdir -p "$BCL2FASTQ_PATH" | |
mkdir -p "$FASTQC_PATH" | |
} | |
make_output_directories; | |
make_sample_sheet; | |
make_bcl2fastq_pbs; | |
qsub -N "B2F_$NAME" $PBS_PATH |
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