pipeline of analyses to identify functional loops of chromosomes
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9.0 years ago
schmilblik ▴ 20

Hello stars,

I want to write a pipeline to predict functional loops of chromosomes Using available Hi-C data, and also RNA-seq and ChIP-seq data?

Any suggestions?

Thanks in advance

RNA-Seq ChIP-Seq • 2.0k views
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9.0 years ago
Ying W ★ 4.3k

The methods of this recent paper have a lot of manual transformations required. Pipelines are usually more common when a method becomes more established. My guess is that not that much high quality Hi-C data has been generated by enough different labs that everyone just does their own thing.

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9.0 years ago
Fidel ★ 2.0k

Using ChIP-seq data you may find evidence for loops as reported by Liang, J et a. (2014), but you can hardly know the actual loop pairs. For RNA-seq data I haven't heard of a method. As for Hi-C there is no consensus on what exactly a loop is. In the papers from Liberman Aiden([1], [2]), loops are defined as CTCF pairs that result in a noticeable enrichment of contacts with respect to background. However, to detect this type of loops a particular method of Hi-C, called In-situ Hi-C, is required, otherwise the signal is very faing. There are other methods to detect contact enrichments that work by identifying pairs of genomic loci that share an enriched number of Hi-C contacts with respect to a background as for example [3], [4]. To identify loops also 4C is commonly used.

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