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Old 07-05-2011, 01:05 AM   #1
HTFRIEDELFF
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Location: madrid

Join Date: Oct 2010
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Default CLC bio Genomics and miRNA nomenclature

Dear all,

we are working on analysis of High Throughput sequencing Data from mIRNA analysis. For that reason, we decided to try it with CLC BIO Genomics Workbench. All the steps were very easy and succesfull, but after a detailed analysis of alignments we found a tricky thing.

When we analysed some miRNA genes, we found that CLC Bio called "precursor" any sequences that mapped in th region of a "mature" along the reference precursor. We dont understand why ClC Bio performed that nomenclature. We think that it should be mature (sub or super or sub/super or whaterver...) because is mapping in the "mature" region.

Other circumstance is that CLC BIo neve calls miRNA genes by their respectives names. I mean, if one gene is 292 and it has been defined two mature structures as 292-5p and 292-3p, why sequences that mapped in both are called in a different way? Those sequences that mapped in 292-5p were called "mature" and those sequences that mapped in 292-3p were called "precursor". I think CLC Bio should be call both as "mature" but making differences in the gene name.

I hope if anybody knows why CLC Bio has this behaviour I will be very gratefull because our experiments try to define differences in miRNA variantions at that level.

Thank you very much!!
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Old 07-05-2011, 05:00 AM   #2
GenoMax
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Location: East Coast USA

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Someone on this list may have an answer for you, but you may want to email CLC biosupport "support@clcbio.com" simultaneously about this question.
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