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Old 09-30-2019, 01:37 PM   #1
leitouran
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Location: Argentina

Join Date: Sep 2019
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Default Artemis paired end illumina short read mapping won't display any "duplicate" reads

Hi! I'm working with Illumina paired end short reads fastq mapping using Artemis for a course I'm taking. While I'm able to get all SAM/BAM files without errors, I noticed my mapping visualization on Artemis looks different than it should: I understand (From the manual and various online tutorials) that there should be blue (unique reads) and green (dupliate reads) stacks on the BAM panel, but I only get blue ones (even for actual duplicated reads).

Has anyone experienced anything like this?
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