Hi everyone. I have to analyze some paired end reads coming from a Illumina MiSeq experiment. What I want to do is removing duplicate reads that not only have the same start-end coordinates but also have 100% sequence identity. Is there any tool that can help me do that? I want to work with BAM files not with FastQ files. Thanks!
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If sequences have 100% identity then they should have the same mapping coordinates, so there's no reason to work with bam files in this case. I wrote a program that can do this for fastq, but not for bam:
dedupe.sh in=reads.fq out=deduped.fq ac=f t=1
There should be tools that can do so on bam files by sorting by sequence, but I don't know what they are offhand.
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