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

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

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

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

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 ??

maybe try miRDeep before DE analysis

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