Question: Differential Rnaseq Expression Analysis Directly On Stanford'S Great?
gravatar for 14134125465346445
6.9 years ago by
United Kingdom
141341254653464453.4k 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 • 2.7k views
ADD COMMENTlink modified 6.6 years ago by Ying W3.9k • written 6.9 years ago by 141341254653464453.4k
gravatar for Ying W
6.9 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k 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 6.9 years ago by Ying W3.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2111 users visited in the last hour