Commit 60579024 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

add control genome comments for CUT& data

parent f5be3025
......@@ -308,7 +308,7 @@ intersectionApproach:
### Default mode for CUT&RUN/CUT&Tag
With CUT&RUN/CUT&Tag data, make deduplication only on INPUT/IgG data (dedup_IP to False). Then perform a stringent peak calling with SEACR and use Intersection Approach. Overlapping parameter of IA on peaks is set at 0.8.
With CUT&RUN/CUT&Tag data, make deduplication only on INPUT/IgG data (dedup_IP to False). Then perform a stringent peak calling with SEACR and use Intersection Approach. Overlapping parameter of IA on peaks is set at 0.8. If data has spike-in, set seacr normalization to non.
```
mark_duplicates:
......
......@@ -58,7 +58,7 @@ design:
marks: K4Me3
condition: C, U
replicates: Rep
spike: yes
spike: no
spike_genome_file: /path/to/genome/directory/dmel9.fa
#===============================================================================
......@@ -304,7 +304,7 @@ bamCoverage:
#===============================================================================
geneBody:
do: yes
do: no
regionsFileName: /path/to/genome/directory/mm10_genemodel.bed
threads: 4
......
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