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==Mapping with BWA == *New BWA read mapping using the script: [[Media:batch_bwa_fastq2bam.txt|batch_bwa_fastq2bam.pl]] *Bowtie2 read mapping using the script: [[Media:batch_fastq2bam.txt|batch_fastq2bam.pl]] *Mapping in Eric_15T/HL163/BWA folder nohup batch_bwa_fastq2bam.pl hg19 > EC_PGP1_21_BWA_batch_fastq2bam.log & *Gather coverage statistics get_covstats.pl > EC_PGP1_21_BWA_covStat.txt & grep rmdupse EC_PGP1_BWA_batch_fastq2bam.log wc -l *targetcut.out grep -B1 'Version' EC_PGP1_BWA_batch_fastq2bam.log|grep -v 'Version' *copy and paste to excel sheet1 and then text separate =OFFSET(Sheet1!$B$1,(ROW()-1)*4,0)
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