Mirna expression analysis

[moriah]

Hi !

I am pretty new at this ...

I have a merged bam file of about 100 patients mirna's and I would like to run an analysis to determine whether there are mirna's the have higher expression than others...

I've heard about Degseq, EdgeR and cufdiff but since I am not familiar with expression analysis I am not sure what is best for me to use.

Can someone suggest some kind of pipeline of working with bam files in order to determine the expression?

Thanks!

[bhill]

Hello,

GenePattern provides a suite of RNAseq modules as well as differential expression modules which may provide an answer to your question.

So that we may better suggest tools for you, can you provide a few more details regarding the sort of expression analysis you would like to do?

Best

Barbara Hill
Cancer Informatics Development
Broad Institute of Harvard and MIT
Cambridge, MA

[moriah]

Thanks for your answer, I will take a look at this.

I would like to test mirna expression in a set of cancer patients ...

[moriah]

Thanks for your answer, I will take a look at this.

I would like to test mirna expression in a set of cancer patients ...