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-   -   Comparison of two sets of miRNAs (http://seqanswers.com/forums/showthread.php?t=18824)

Giorgio C 03-30-2012 04:02 AM

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

NicoBxl 03-30-2012 06:32 AM

which type of data ? explain a little bit more about your problem

Giorgio C 03-30-2012 07:31 AM

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

NicoBxl 03-30-2012 07:37 AM

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

Giorgio C 03-30-2012 07:39 AM

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 ??

NicoBxl 03-30-2012 07:42 AM

maybe try miRDeep before DE analysis

Giorgio C 03-30-2012 07:47 AM

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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