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Old 04-30-2013, 02:03 AM   #1
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Default how to calculate genome coverage correcting for multiple genome hits

Hi everybody,
thanks for all the useful posts I found in this blog that helped me for my work.

I am new to bioinformatics and I have a question about multiple genome hits. I work with smallRNA-seq form maize; I would like to calculate the genome coverage taking into account not only reads mapping univocally to the genome but also reads with multiple hits in the genome. I did not find a tool that allow to normalize the coverage by diving, for each read's position, it's coverage to the number of alignments the read has on genome.

I thank everybody that could help me on that issue!


Last edited by alice.lunardon; 05-01-2013 at 02:20 PM.
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