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Old 09-21-2010, 01:57 AM   #3
Junior Member
Location: Cambridge, UK

Join Date: Nov 2009
Posts: 6
Default Detecting alignment collapse


I want to check my genome sequence for collapsed, tandemly repeated genes. It seems to me that I could use software for detecting CNVs in that I am looking for significantly increased read depth. CNV-seq requires test and reference sequences, which makes sense to control for sequence-based noise in read depth however I only have my reference genome and one instance of Illumina data. Does anyone have any ideas?

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