Hi, I get a file named *.allValidPairs. I also set the option GET_PROCESS_SAM to 1 in order to get the bam file. I browse these issues created by other researchers about how to convert .allValidPairs file to bam file, and I notice `.bwt2pairs_interaction.bamdosen't remove duplicated reads pairs. So I want to create a valid bam file without duplication. I can filter*.bwt2pairs_interaction.bam` to keep on valid pairs with duplication by using samtools. Could you please give me some advices about this problem ?
Hi, I get a file named
*.allValidPairs. I also set the optionGET_PROCESS_SAMto 1 in order to get the bam file. I browse these issues created by other researchers about how to convert .allValidPairs file to bam file, and I notice `.bwt2pairs_interaction.bamdosen't remove duplicated reads pairs. So I want to create a valid bam file without duplication. I can filter*.bwt2pairs_interaction.bam` to keep on valid pairs with duplication by using samtools. Could you please give me some advices about this problem ?Thanks a lot!