Changes between Version 16 and Version 17 of SOPs/CUT&Tag

Timestamp:

11/08/24 14:02:43 (2 months ago)

Author:

ibarrasa

Comment:

--

SOPs/CUT&Tag

@@ -31 +31 @@
 }}}
 
+These are our recommended options:
+{{{
+--end_to_end FALSE  
+--save_spikein_aligned  TRUE  
+--save_align_intermed  TRUE 
+--skip_removeduplicates true  
+--skip_preseq false   
+--skip_dt_qc false 
+--skip_multiqc false 
+--skip_reporting false 
+--dump_scale_factors true
+--normalisation_binsize 1 (default 50) 
+}}}
+
+To run macs2 using the "--keep-dup auto" setting you can use a input a profile file like the one described below:
+macs2CustomCUTRUN.config
+{{{
+process {
+    withName: '.*:CUTANDRUN:MACS2_.*' {
+        ext.args   = [
+            '--keep-dup auto',
+            '--nomodel',
+            '--shift -75',
+            '--extsize 150',
+            '--format BAM',
+            '--bdg ',
+            '--qvalue 0.01'
+        ].join(' ').trim()
+
+    }
+}
+}}}
+
+The command to be run with that file would be:
+{{{
+sbatch --partition=20 --job-name=NextF --output=NextF-%j.out  --mem=300gb   --nodes=1 --ntasks=1 --cpus-per-task=20 --wrap \
+nextflow run nf-core/cutandrun -profile singularity --normalisation_binsize 1  --input ./samplesheet.csv -c macs2CustomCUTRUN.config  --normalisation_mode CPM \
+--save_align_intermed  TRUE --peakcaller 'MACS2' --replicate_threshold 2  --end_to_end FALSE  --multiqc_title 'multiQCReport' --skip_removeduplicates true \
+--skip_preseq false   --skip_dt_qc false --skip_multiqc false --skip_reporting false --dump_scale_factors true --email 'username@wi.mit.edu' --genome GRCh38 \
+--extend_fragments false --macs2_qvalue 0.01 --outdir  ./nextFlow_macs2auto  "
+}}}
 
 
 Pipeline reference pages:
-
 [https://github.com/nf-core/cutandrun/ nf-core CUT&Tag pipeline]