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jzhoulab / puffin_manuscript

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Question on the resources.tar.xz #2

Closed wgmao closed 1 week ago

wgmao commented 1 week ago

Thank you for keeping things organized! I was able to download the resource files following the instructions. After browsing the files included, I have a couple of questions regarding the following files: agg.minus.bw.bedgraph.bw and agg.plus.bw.bedgraph.bw.

  1. My understanding is that these two files are strand-specific CAGE profiles after aggregation. If so, are they based on the CAGE profiles from FANTOM, ENCODE or both cohorts? Additionally, what raw profiles were included to generate these two tracks?
  2. Do these profiles correspond to the experimental track on the web portal at https://puffin.zhoulab.io/?

Thanks!

jzthree commented 1 week ago
  1. These are the aggregated strand-specific FANTOM CAGE files. Essentially all human CAGE files from https://fantom.gsc.riken.jp/5/datafiles/latest/basic/ but not including LQhCAGE. We have separate bw files for ENCODE CAGE and other techniques.
  2. Yes
wgmao commented 1 week ago

Thank you!