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  • quantification of noncoding RNA by Cufflink

    I was wondering if some one has used Top hat aligned RNA-seq reads to quantify differential expression cf noncoding RNA between case and control samples.
    Thanks

  • #2
    I haven't used it, but i guess it should not be any different, in comparison to coding genes. As long as RNASeq captures ncRNA expression, the use of tophat and cufflink should be able to tell you the use of differential expression. However, the lower expression (in general) level of ncRNA, might not give the better picture of differential expression, unless you have a very high coverage.

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