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demultiplexing C4G9YACXX
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| #!/bin/bash | |
| # load modules | |
| module load bcl2fastq/gnu/1.8.4 | |
| CORES=12 | |
| EMAIL='lg1883@nyu.edu' | |
| BASECALLS="/scratch/gencore/manual/140617_SN911_0218_AC4G9YACXX/Data/Intensities/BaseCalls/" | |
| FASTQ_BASE="/scratch/gencore/manual" | |
| SAMPLE_SHEET_HEAD="FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject" | |
| BCL_TO_FASTQ_CMD="/share/apps/bcl2fastq/1.8.4/gnu/bin/configureBclToFastq.pl" | |
| PBS_HEAD=" | |
| #!/bin/sh | |
| #PBS -V | |
| #PBS -l nodes=1:ppn=$CORES,walltime=48:00:00 | |
| #PBS -M $EMAIL | |
| #PBS -m abe | |
| #PBS -q s48 | |
| #PBS -l mem=16GB | |
| module load ncurses/gnu/5.9 | |
| module load bcl2fastq/gnu/1.8.4 | |
| " | |
| PBS_FOOT=" | |
| make -j$CORES | |
| exit $?; | |
| " | |
| make_bcl2fastq_pbs() { | |
| BCL_To_FASTQ_RUN=$1 | |
| echo -e "$PBS_HEAD | |
| cd $FASTQ_BASE/$BCL_To_FASTQ_RUN/Unaligned | |
| $PBS_FOOT$" > $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs | |
| } | |
| make_sample_sheet(){ | |
| BCL_To_FASTQ_RUN=$1 | |
| echo -e "$SAMPLE_SHEET_HEAD | |
| $2" > $FASTQ_BASE/$BCL_To_FASTQ_RUN/SampleSheet.csv | |
| } | |
| # RUN | |
| BCL_To_FASTQ_RUN="140617_SN911_0218_AC4G9YACXX_DUAL" | |
| mkdir -p "$FASTQ_BASE/$BCL_To_FASTQ_RUN" | |
| make_bcl2fastq_pbs "$BCL_To_FASTQ_RUN" | |
| make_sample_sheet $BCL_To_FASTQ_RUN "\ | |
| C4G9YACXX,5,Nextera-97,,TAAGGCGA-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-98,,TAAGGCGA-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-99,,TAAGGCGA-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-100,,TAAGGCGA-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-101,,TAAGGCGA-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-102,,TAAGGCGA-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-103,,TAAGGCGA-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-104,,TAAGGCGA-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-105,,CGTACTAG-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-106,,CGTACTAG-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-107,,CGTACTAG-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-108,,CGTACTAG-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-109,,CGTACTAG-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-110,,CGTACTAG-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-111,,CGTACTAG-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-112,,CGTACTAG-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-113,,AGGCAGAA-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-114,,AGGCAGAA-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-115,,AGGCAGAA-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-116,,AGGCAGAA-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-117,,AGGCAGAA-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-118,,AGGCAGAA-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-119,,AGGCAGAA-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-120,,AGGCAGAA-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-121,,TCCTGAGC-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-122,,TCCTGAGC-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-123,,TCCTGAGC-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-124,,TCCTGAGC-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-125,,TCCTGAGC-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-126,,TCCTGAGC-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-127,,TCCTGAGC-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-128,,TCCTGAGC-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-129,,GGACTCCT-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-130,,GGACTCCT-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-131,,GGACTCCT-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-132,,GGACTCCT-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-133,,GGACTCCT-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-134,,GGACTCCT-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-135,,GGACTCCT-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-136,,GGACTCCT-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-137,,TAGGCATG-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-138,,TAGGCATG-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-139,,TAGGCATG-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-140,,TAGGCATG-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-141,,TAGGCATG-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-142,,TAGGCATG-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-143,,TAGGCATG-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-144,,TAGGCATG-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-145,,CTCTCTAC-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-146,,CTCTCTAC-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-147,,CTCTCTAC-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-148,,CTCTCTAC-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-149,,CTCTCTAC-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-150,,CTCTCTAC-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-151,,CTCTCTAC-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-152,,CTCTCTAC-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-153,,CAGAGAGG-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-154,,CAGAGAGG-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-155,,CAGAGAGG-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-156,,CAGAGAGG-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-157,,CAGAGAGG-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-158,,CAGAGAGG-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-159,,CAGAGAGG-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-160,,CAGAGAGG-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-161,,GCTACGCT-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-162,,GCTACGCT-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-163,,GCTACGCT-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-164,,GCTACGCT-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-165,,GCTACGCT-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-166,,GCTACGCT-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-167,,GCTACGCT-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-168,,GCTACGCT-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-169,,CGAGGCTG-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-170,,CGAGGCTG-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-171,,CGAGGCTG-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-172,,CGAGGCTG-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-173,,CGAGGCTG-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-174,,CGAGGCTG-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-175,,CGAGGCTG-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-176,,CGAGGCTG-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-177,,AAGAGGCA-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-178,,AAGAGGCA-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-179,,AAGAGGCA-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-180,,AAGAGGCA-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-181,,AAGAGGCA-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-182,,AAGAGGCA-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-183,,AAGAGGCA-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-184,,AAGAGGCA-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-185,,GTAGAGGA-TAGATCGC,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-186,,GTAGAGGA-CTCTCTAT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-187,,GTAGAGGA-TATCCTCT,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-188,,GTAGAGGA-AGAGTAGA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-189,,GTAGAGGA-GTAAGGAG,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-190,,GTAGAGGA-ACTGCATA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-191,,GTAGAGGA-AAGGAGTA,,N,,Wei Yuan,Athaliana_finemapping | |
| C4G9YACXX,5,Nextera-192,,GTAGAGGA-CTAAGCCT,,N,,Wei Yuan,Athaliana_finemapping | |
| " | |
| echo -e "$BCL_TO_FASTQ_CMD --input-dir $BASECALLS \ | |
| --output-dir $FASTQ_BASE/$BCL_To_FASTQ_RUN/Unaligned \ | |
| --sample-sheet $FASTQ_BASE/$BCL_To_FASTQ_RUN/SampleSheet.csv \ | |
| --fastq-cluster-count 0 \ | |
| --use-bases-mask \"Y*,I8,I8,Y*\" \ | |
| --tiles \"s_5\" \ | |
| --no-eamss \ | |
| --mismatches 1"|bash | |
| qsub -N $BCL_To_FASTQ_RUN $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs | |
| BCL_To_FASTQ_RUN="140617_SN911_0218_AC4G9YACXX_SINGLE" | |
| mkdir -p "$FASTQ_BASE/$BCL_To_FASTQ_RUN" | |
| make_bcl2fastq_pbs "$BCL_To_FASTQ_RUN" | |
| make_sample_sheet $BCL_To_FASTQ_RUN "\ | |
| C4G9YACXX,2,1L22A,,ATCACG,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,3L22A,,CGATGT,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,13L22A,,TTAGGC,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,20L22A,,TGACCA,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,1L15A,,ACAGTG,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,3L15A,,GCCAAT,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,13L15A,,CAGATC,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,20L15A,,ACTTGA,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,1S15A,,GATCAG,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,3A15A,,TAGCTT,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,13S15A,,GGCTAC,,N,,Karen Hicks,moss | |
| C4G9YACXX,2,20S15A,,CTTGTA,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,1L22B,,ATCACG,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,3L22B,,CGATGT,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,13L22B,,TTAGGC,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,20L22B,,TGACCA,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,1L15B,,ACAGTG,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,3L15B,,GCCAAT,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,13L15B,,CAGATC,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,20L15B,,ACTTGA,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,1S15B,,GATCAG,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,3A15B,,TAGCTT,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,13S15B,,GGCTAC,,N,,Karen Hicks,moss | |
| C4G9YACXX,3,20S15B,,CTTGTA,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,1L22C,,ATCACG,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,3L22C,,CGATGT,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,13L22C,,TTAGGC,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,20L22C,,TGACCA,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,1L15C,,ACAGTG,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,3L15C,,GCCAAT,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,13L15C,,CAGATC,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,20L15C,,ACTTGA,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,1S15C,,GATCAG,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,3A15C,,TAGCTT,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,13S15C,,GGCTAC,,N,,Karen Hicks,moss | |
| C4G9YACXX,4,20S15C,,CTTGTA,,N,,Karen Hicks,moss | |
| C4G9YACXX,6,SDW_HiSeq_1,,CGATGT,,N,,Sally Warring,Tvag_RNASseq | |
| C4G9YACXX,6,SDW_HiSeq_2,,TGACCA,,N,,Sally Warring,Tvag_RNASseq | |
| C4G9YACXX,6,SDW_HiSeq_3,,ACAGTG,,N,,Sally Warring,Tvag_RNASseq | |
| C4G9YACXX,6,SDW_HiSeq_4,,GCCAAT,,N,,Sally Warring,Tvag_RNASseq | |
| C4G9YACXX,6,SDW_HiSeq_5,,CTTGTA,,N,,Sally Warring,Tvag_RNASseq | |
| C4G9YACXX,6,SDW_HiSeq_6,,GTGAAA,,N,,Sally Warring,Tvag_RNASseq | |
| C4G9YACXX,7,ZL1,,CGATGT,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL2,,TGACCA,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL3,,ACAGTG,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL4,,GCCAAT,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL5,,CAGATC,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL6,,CTTGTA,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL7,,ATCACG,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,7,ZL8,,TTAGGC,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL1,,CGATGT,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL2,,TGACCA,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL3,,ACAGTG,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL4,,GCCAAT,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL5,,CAGATC,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL6,,CTTGTA,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL7,,ATCACG,,N,,Zunping Luo,Hybrid_Selection | |
| C4G9YACXX,8,ZL8,,TTAGGC,,N,,Zunping Luo,Hybrid_Selection | |
| " | |
| echo -e "$BCL_TO_FASTQ_CMD --input-dir $BASECALLS \ | |
| --output-dir $FASTQ_BASE/$BCL_To_FASTQ_RUN/Unaligned \ | |
| --sample-sheet $FASTQ_BASE/$BCL_To_FASTQ_RUN/SampleSheet.csv \ | |
| --fastq-cluster-count 0 \ | |
| --use-bases-mask \"Y*,I6nn,n*,Y*\" \ | |
| --tiles \"s_2,s_3,s_4,s_6,s_7,s_8\" \ | |
| --no-eamss \ | |
| --mismatches 1"|bash | |
| qsub -N $BCL_To_FASTQ_RUN $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs |
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