Hiii all,
i want to align my paired end data to the ref genome using bowtie. i have used sm cmd like this
bowtie -q -m 1 -3 35 -v 1 ref_genom −1 E1R1.fastq,E2R1.fastq -2 E1R2fastq,E2R2_.fastq result.out
it gave the result tat has all intrachromosomal interactions. i dont think this is the correct result. what should be done to get correct result which would have both inter and intrachromosomal interactions —fr opton i read would be taken as default for paired ends right even if not mentioned
i want to align my paired end data to the ref genome using bowtie. i have used sm cmd like this
bowtie -q -m 1 -3 35 -v 1 ref_genom −1 E1R1.fastq,E2R1.fastq -2 E1R2fastq,E2R2_.fastq result.out
it gave the result tat has all intrachromosomal interactions. i dont think this is the correct result. what should be done to get correct result which would have both inter and intrachromosomal interactions —fr opton i read would be taken as default for paired ends right even if not mentioned