< bis2-noerror.txt # get alignments from bwa-meth that are not in bis2 samtools view -f2 results/bwa-noerrorsim.bam | awk '$5 > 20' | cut -f 1 \ | uniq | grep -vFf bis2-noerror.txt | sort -u > bwa-uniq.txt exit; DONE python src/extract-read.py "10001_chr6:125453407-125453496" \ data/noerrorsim_R1.fastq.gz \ data/noerrorsim_R2.fastq.gz bowtie2 -q -N 1 --score-min L,-0.4,-0.5 --reorder --ignore-quals --no-mixed \ --maxins 600 -x \ /data/Schwartz/brentp/mm10/ref/Bisulfite_Genome/CT_conversion/BS_CT \ -1 o_R1.fq -2 o_R2.fq -q | grep -v "^@" bowtie2 -q -N 1 --score-min L,-0.4,-0.5 --reorder --ignore-quals --no-mixed \ --maxins 600 -x \ /data/Schwartz/brentp/mm10/ref/Bisulfite_Genome/GA_conversion/BS_GA \ -1 o_R1.fq -2 o_R2.fq -q | grep -v "^@"