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Old 08-21-2011, 01:35 AM   #1
moriah
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Location: Israel

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Red face Mirna expression analysis

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!
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Old 08-22-2011, 07:10 AM   #2
bhill
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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
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Old 08-23-2011, 01:35 AM   #3
moriah
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Thanks for your answer, I will take a look at this.

I would like to test mirna expression in a set of cancer patients ...
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Old 08-23-2011, 01:46 AM   #4
moriah
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Thanks for your answer, I will take a look at this.

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