CLC bio Genomics and miRNA nomenclature

HTFRIEDELFF · 07-05-2011, 01:05 AM

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!!

GenoMax · 07-05-2011, 05:00 AM

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
CLC bio - GATK	spreeth84	Bioinformatics	3	02-10-2012 10:41 AM
Annotation of NGS data with CLC Bio	Anelda	Bioinformatics	22	03-29-2011 10:49 AM
Processing SOLiD data with CLC bio Genomics work bench	wishSEQ	RNA Sequencing	4	03-01-2009 05:43 AM
CLC Bio	dcfargo	General	5	09-01-2008 08:25 PM
Hello from CLC bio in Denmark	Roald	Introductions	4	08-28-2008 05:16 AM

07-05-2011, 01:05 AM	#1
HTFRIEDELFF Junior Member Location: madrid Join Date: Oct 2010 Posts: 2	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!!

07-05-2011, 05:00 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	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.