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Old 03-25-2014, 12:55 PM   #1
Bakhtiyar Taghizada
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Location: Toronto, Ontario

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Default Coverage in centromeric regions

I have a sequenced paired end data of S.cerevisisae, sequenced by Illumina, I was wondering why there is low coverage in the centromeric regions compared to the rest of the genome. There are centromeric regions that even do not have any coverage. My average coverage is 30, and the reads are 100bp long. The fragments that was sequenced had a length of 600bp (reads are 100bp form one end and 100bp from other , paired reads)
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Old 03-27-2014, 05:57 AM   #2
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Centromeric regions contain repeats. Aligners put reads to one position, even if the read can be aligned to several places. See the program's documentation to change this behviour.
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