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  • Mapping genomic regions promoter 3' UTR exon etc

    I have a list of differentially expressed genes/ transcripts from an RNA-seq data. what I would like to understand is that how the distribution of reads is corresponding to promoter 5'UT,exon,3'UTR etc. in my two samples Treated vs control. I have seen several ChIP-seq papers have reported something like on similar lines. Once we have enriched peaks then it is found out whether that enriched region is in promoter or not. However what tool can be used in RNA-seq read count data? I would like to have list of genes where reads are more in one particular genomic region- promoter, UTR etc.

    Any suggestion please. If my question is not very clear please advice I will try to come up with more details, sometime you feel you are so much involved in the project that you think you are conveying the message.
    Last edited by mathew; 05-10-2012, 07:43 PM.

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