Changes between Version 11 and Version 12 of SOPs/CUT&Tag

Timestamp:

05/06/24 16:07:03 (13 days ago)

Author:

ibarrasa

Comment:

--

SOPs/CUT&Tag

@@ -17 +17 @@
 To run the analysis for the same example input with one command using **nextflow** run the following commands on fry
 {{{
- 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  --normalisation_mode RPGC --igg_scale_factor 1 --peakcaller 'MACS2'    --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 0.1 --minimum_alignment_q_score 0 --outdir  ./OutNextF_keepAllReads_RPGC_q0  "
+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  " /nfs/BaRC_Public/apps/nextflow/nextflow run nf-core/cutandrun   -profile singularity  --input /nfs/BaRC_Public/Hot_Topics/CUTandTag/nextFlow/samplesheet.csv  --normalisation_mode CPM --igg_scale_factor 1 --peakcaller 'MACS2'    --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 0.1 --minimum_alignment_q_score 0 --outdir  ./OutNextF_keepAllReads_CPM_q0  "
+
+###Alternative more stringent peak calling
+#Change these parameters to increase the stringency:
+# --minimum_alignment_q_score 20  #to filter out low quality mapping 
+#and
+# --macs2_qvalue 0.01 or 0.001 #to increase macs2 stringency
+
+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_Public/Hot_Topics/CUTandTag/nextFlow/samplesheet.csv  --normalisation_mode CPM --igg_scale_factor 1 --peakcaller 'MACS2'    --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 --minimum_alignment_q_score 20 --outdir  ./OutNextF_keepAllReads_CPM_q20  "
 }}}
 
-Change these parameters to increase the stringency:
- --minimum_alignment_q_score 20  #to filter out low quality mapping 
-and
- --macs2_qvalue 0.01 or 0.001 #to increase macs2 stringency
+
 
 Pipeline reference pages: