Question: Differential Rnaseq Expression Analysis Directly On Stanford'S Great?
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5.2 years ago by
United Kingdom
141341254653464453.2k wrote:

Does anybody know if the tool GREAT from Stanford U. can be used for RNAseq differential expression analysis directly from BAM/bed files of the reads aligned from the two experimental conditions? Or is it better to run preprocess the data through another tool beforehand?

gene-expression rna-seq • 1.9k views
ADD COMMENTlink modified 4.9 years ago by Ying W3.6k • written 5.2 years ago by 141341254653464453.2k
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gravatar for Ying W
5.2 years ago by
Ying W3.6k
South San Francisco, CA
Ying W3.6k wrote:

i believe GREAT is used for chip-seq data not RNAseq data, they seem to want you to upload two bed files, one bed file of significantly enriched regions from chip-seq and another of background. you would probably have to generate these by using a peak caller. From a brief glance, it seems like they take these regions and see if function of nearby genes are similar so I am not quite sure how you would use this with RNA-seq data since you would expect most peaks to be over exons

ADD COMMENTlink written 5.2 years ago by Ying W3.6k
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