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crazyhottommy / ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang
MIT License
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Can ROSE handle multiple samples together? #11

Closed biobug16 closed 4 years ago

biobug16 commented 4 years ago

Hi @crazyhottommy I am trying to use ROSE to call Super Enhancer between the two subtypes of a cancer, where each group has 5 samples. But I am not sure how to identify potential SE by handling multiple samples (together with ROSE) from each subtype and to compare these with the other subtype. Do you have any suggestions, I'll really appreciate your help. Thanks

crazyhottommy commented 4 years ago

you may want to merge 5 samples' bam files to a single one then call superEnhancer using ROSE or you call each individual bam SuperEnhancers and then use bedtools to find the common ones in each subtype and then compare across subtypes.