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Old 03-30-2012, 03:02 AM   #1
Giorgio C
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Default Comparison of two sets of miRNAs

Hi all,

i have two sets A and B of miRNAs. How i can make a comparison of them considering common elements and not ?

Is there any tool that makes this type of comparison ?

Thanks in advance for your help
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Old 03-30-2012, 05:32 AM   #2
NicoBxl
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which type of data ? explain a little bit more about your problem
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Old 03-30-2012, 06:31 AM   #3
Giorgio C
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There are two sets of miRNAs one coming out from a leaf and the other from the flower of the same Orchid. I have to know what are the differences between these two sets:
Elements in common and not. They are both in fasta format and in replicate (trimmed, filtered and collapsed with galaxy tools) originally coming out from a 454 platform.

they apper like this:

>1-8490
ACGTCACTCTCTCC..
>2-7990
CGTCAATCGCCTCC..
>3-6696
ACGTGCACTGCATG..

the first number is the Id , the second represents the number of occurences.

I need to evidence what are the differences fromt he two sets. Do you have any advice ??

tnx
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Old 03-30-2012, 06:37 AM   #4
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Ok


First annotate your reads : align them against mirbase databse (with blats per example) and then count for each miR, the number of reads.

After that in R create a matrix : each line represent one miR, each column a sample. Then use DESeq or edgeR for the DE analysis
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Old 03-30-2012, 06:39 AM   #5
Giorgio C
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thank you very much for your fast reply. Is a problem that most of the miRNAs are novel and have no match with the database ??
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Old 03-30-2012, 06:42 AM   #6
NicoBxl
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maybe try miRDeep before DE analysis
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Old 03-30-2012, 06:47 AM   #7
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Yes, i'v just done it with mirDeep but being this type of Orhichid not yet annotated i have a lot of no matching elements
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