remove duplicate reads 100% sequence identity and genomic coordinates

thiNGS · 01-12-2015, 06:59 AM

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!

Brian Bushnell · 01-12-2015, 09:53 AM

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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01-12-2015, 06:59 AM	#1
thiNGS Member Location: Netherlands Join Date: Sep 2014 Posts: 24	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!

01-12-2015, 09:53 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	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.