How to identify differential enhancers?
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6 weeks ago
2973520704 • 0

Deseq2 or edgeR only allow the input of reads count to identify differential regions, but I get less differential enhancer with reads count, can I use the signal from the bigwig file as input to deseq2 or edgeR to identify the differential enhancer?

EdgeR ChIP-seq Bigwig Differential enhancer Deseq2 • 322 views
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See the DiffBind or csaw documentation.

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Ok, thank you very much!

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5 weeks ago
ATpoint 57k

No, the scores in bigwig files are not suitable for differential expression. The exact count information, so how many independent reads overlap a given region is lost. You have to create these counts from the BAM files.

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