Hello. I have a Fastq file with 30,000 reads. When I analyze them with Fastqc the level of duplicates goes very high. Then I trim the readings to eliminate low quality bases and the levels of duplicates drop to normal levels. I suppose this will be because when I change the length of the readings the program doesn't consider them as duplicates. Then I map the readings with Bowtie2 and I pass the BAM file to MarkDuplicates. Almost all the sequences are mapped but PERCENT DUPLICATION go back up to 80%. How can this be? Thank you.
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Question: (Closed) Problem with Percent duplication on MARK DUPLICATES
4 months ago by
julieta • 10
julieta • 10 wrote:
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