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update README
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lldelisle committed Sep 1, 2023
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Expand Up @@ -9,14 +9,16 @@ The goal of this workflow is to get a list of confident peaks with summits from
## Inputs values

- effective_genome_size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).
- bin_size: this is the bin sized used to compute the average of normalized profiles. Large values will allow to have a smaller output file but with less resolution while small values will increase computation time and size of the output file to produce a more resolutive bigwig.

## Processing

- The workflow will:
- on the one hand,
- call peaks on each BAM (or BED) individually
- compute the intersection between both
- on the other hand,
- first part:
- call peaks and compute normalized coverage on each BAM (or BED) individually
- average normalized profiles
- compute the intersection between both peaks
- second part:
- subset both BAM (or BED) to get the same number of reads
- call peaks on both subsetted BAM combined
- finally, keep only peaks from the second part that have summits overlapping the intersection of the first part.

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