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Old 01-12-2015, 06:59 AM   #1
thiNGS
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Default remove duplicate reads 100% sequence identity and genomic coordinates

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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Old 01-12-2015, 09:53 AM   #2
Brian Bushnell
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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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