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@fansalon fansalon released this 06 Oct 13:17
· 58 commits to main since this release
1.0.0
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Learn about vigilant mode.

In this new version of the CUT&Tag pipeline, a bedgraph file containing normalized signal is generated, in addition to all the other files that were generated from the previous pipeline version.

The pipeline now:

  • generates the un-normalized bedgraph file as it did before (--> aligned/bedgraph/raw)
  • generates, in addition, a new bedgraph file where the signal is normalized on the number of million mapped reads (retrieved from Picard MarkDupl metrics file) (--> aligned/bedgraph/normalized)

Peak calling by SEACR can then be performed on the raw or normalized bedgraph file. Nothing changes in terms of peak coordinates, but it does change in terms of signal associated to the peaks as in one case it will derive from raw signal, and in the other from normalized signal.

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