SEQanswers (
-   Bioinformatics (
-   -   Comparison of two sets of miRNAs (

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:


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 ??


NicoBxl 03-30-2012 07:37 AM


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

All times are GMT -8. The time now is 07:20 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.