#bwa aln -t 32 -N data/ecoli.fa ../../data/EC_ECOLI_MC_READS/corrected/mc.orig.2.fq.00.cor.fastq > data/ec2.sai
#bwa aln -t 32 -N data/ecoli.fa ../../data/EC_ECOLI_MC_READS/corrected/mc.orig.1.fq.00.cor.fastq > data/ec1.sai
6.2/bwa aln -t 32 -N data/ecoli.fa ../../data/ECOLI/mc.orig.1.fq > data/ec1.sai
6.2/bwa aln -t 32 -N data/ecoli.fa ../../data/ECOLI/mc.orig.2.fq > data/ec2.sai
#bwa sampe -n 10000 data/ecoli.fa data/ec1.sai data/ec2.sai ../../data/EC_ECOLI_MC_READS/corrected/mc.orig.1.fq.00.cor.fastq ../../data/EC_ECOLI_MC_READS/corrected/mc.orig.2.fq.00.cor.fastq > data/ec.sam
6.2/bwa sampe -n 10000 data/ecoli.fa data/ec1.sai data/ec2.sai ../../data/ECOLI/mc.orig.1.fq ../../data/ECOLI/mc.orig.2.fq > data/ec.sam
samtools view -bS ec.sam | samtools sort - ec
samtools index ec.bam

