Changes between Version 12 and Version 13 of SOPs/CUT&Tag

Timestamp:

05/13/24 09:58:40 (9 months ago)

Author:

gbell

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  " /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  "
+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
@@ -27 +27 @@
 # --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  "
+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"
 }}}