Changes between Version 5 and Version 6 of SOPs/CUT&Tag

Timestamp:

04/22/24 16:44:49 (10 months ago)

Author:

ibarrasa

Comment:

--

SOPs/CUT&Tag

@@ -14 +14 @@
 
 For a working example for how to run the published analysis workflow using the computing resources at the Whitehead Institute, please follow /nfs/BaRC_Public/BaRC_code/pipelines/analyze_CUTnTag/README and find the associated scripts within the parent directory.
+
+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  --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  "
+}}}
+
+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:
+ --minimum_alignment_q_score 20  #to filter out low quality mapping 
+and
+ --macs2_qvalue 0.01  #to remove low confidence peaks
+
+For other setting to use on the nfcore pipeline check these links:
+
+https://github.com/nf-core/cutandrun
+https://nf-co.re/cutandrun/3.2.2/parameters
+