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Creating a BedGraph file for STRAND-SPECIFIC short read data

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  • Creating a BedGraph file for STRAND-SPECIFIC short read data

    Hi,

    does anyone know a tool or program that can create a density profiles across the genome (I assume bedGraph would be the best format) that deals with strand-specific data e.g. RNA-seq reads from Helicos (this is not what I have, so please dont give me a Helicos-specific answer!!). I have reads whose strand I know and I want to see density profiles of positive and negatively mapping strands. Preferably from a Bowtie alignment but I can convert formats if necessary

    thanks!
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