Hi - does not sound as a BioC question but I will be happy to answer: miRNA 
filtering is important because many processed tRNAs, snoRNAs, piRNAs etc are 
highly similar to known miRNAs. Hence their presence will screw up your 
counts

Kind regards

Alessandro
-----------------------------------------------------
Alessandro Guffanti - Bioinformatics, Genomnia srl
Via Nerviano, 31 - 20020 Lainate, Milano, Italy
Ph: +39-0293305.702 Fax: +39-0293305.777
http://www.genomnia.com
"If you can dream it, you can do it" (Walt Disney)

-----Original Message-----
 From: "Wu, Huiyun" <william.wu@vanderbilt.edu>
 To: "bioconductor@r-project.org" <bioconductor@r-project.org>
 Date: Wed, 16 May 2012 15:52:00 -0500
 Subject: [BioC] miRNA and other small RNAs


Dear users,

 I have a question about miRNA differential profiling between two groups. 
Someone suggested a further filtering of other small RNAs such as mRNA 
degradation, etc with lengths similar to miRNA after BAM file (which 
pre-filtering out longer or shorter ones) read-in. I was wondering what 
consequences would be if I do NOT conduct this process. In this situation, a 
miRNA count table contains those contaminated non-coding small RNAs and 
those small RNAs are brought into DE analysis. My intuitive understanding is 
that it should be fine as long as the miRNA IDs (say, Entrez IDs)are not 
shared by other small RNAs during alignment or annotation.

 thanks in advance.

 sincerely,

 William Wu

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