Which file do I use as the result?

YeoLab / merge_peaks

Pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks

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Which file do I use as the result? #4

Closed XudongHan-bio closed 3 years ago

XudongHan-bio commented 3 years ago

In the result, there are mainly .idr.out, .idr.out.normed.bed and .custombed files. According to Supplementary Protocol 2: eCLIP-seq Processing Pipeline, the .custombed file should be the final result and contain individual replicate information. However, in the Readme, file *.custombed is told that it cannot be used. So in which file should I use the results to annotate genes? If I can get a reply, I would be extremely grateful.

byee4 commented 3 years ago

The custombed files should have the same information as what's in the paper, so they can be used. However since BED is a more acceptable standard, we recommend using that as a "final" result.