Changes between Version 7 and Version 8 of SOPs/CUT&Tag

Timestamp:

04/23/24 14:55:02 (9 months ago)

Author:

ibarrasa

Comment:

--

SOPs/CUT&Tag

@@ -19 +19 @@
  mkdir /nfs/BaRC_training/CUTTAG/yourUserName
  cd /nfs/BaRC_training/CUTTAG/yourUserName
- sbatch --partition=20 --job-name=NextF_CT --output=NextF_CT_1sample-%j.out  --mem=150gb   --nodes=1 --ntasks=1 --cpus-per-task=20 --wrap  " ../bin/nextflow run nf-core/cutandrun   -profile singularity  --input /nfs/BaRC_training/CUTTAG/nextFlow/samplesheet.csv  --normalization_mode RPGC --igg_scale_factor 1 --peakcaller 'MACS2'    --multiqc_title 'multiQCReport' --skip_removeduplicates true  --skiq_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 0.1 --minimum_alignment_q_score 0 --outdir  ./OutNextF_keepAllReads_RPGC_q0  "
+ sbatch --partition=20 --job-name=NextF_CT --output=NextF_CT_1sample-%j.out  --mem=150gb   --nodes=1 --ntasks=1 --cpus-per-task=20 --wrap  " /nfs/BaRC_Public/apps/nextflow/nextflow run nf-core/cutandrun   -profile singularity  --input /nfs/BaRC_training/CUTTAG/nextFlow/samplesheet.csv  --normalization_mode RPGC --igg_scale_factor 1 --peakcaller 'MACS2'    --multiqc_title 'multiQCReport' --skip_removeduplicates true  --skiq_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 --minimum_alignment_q_score 0 --outdir  ./OutNextF_keepAllReads_RPGC_q0  "
 }}}
 
-The setting above will give you the same results as the shell pipeline on /nfs/BaRC_Public/BaRC_code/pipelines/analyze_CUTnTag/README however you may want to consider using:
+Change these parameters to increase the stringency:
  --minimum_alignment_q_score 20  #to filter out low quality mapping 
 and
- --macs2_qvalue 0.01  #to remove low confidence peaks
+ --macs2_qvalue 0.01 or 0.001 #to increase macs2 stringency
 
-For other settings on the nfcore pipeline check these links:
+Pipeline reference pages:
 
-https://github.com/nf-core/cutandrun
-https://nf-co.re/cutandrun/3.2.2/parameters
+[https://github.com/nf-core/cutandrun/ nf-core CUT&Tag pipeline]
+
+[https://nf-co.re/cutandrun/3.2.2/parameters/ CUT&Tag pipeline parameters]