Changes between Version 111 and Version 112 of SOPs/atac_Seq

Timestamp:

11/08/24 14:34:12 (2 months ago)

Author:

ibarrasa

Comment:

--

SOPs/atac_Seq

@@ -295 +295 @@
   * Use housekeeping genes to check QC: signal enrichment is expected in the regulatory regions of housekeeping genes in good ATAC-seq experiments. Use IGVSnapshot function with geneNames param. 
 
+=== Running the nf-core ATAC-seq pipeline===
+* [[https://nf-co.re/atacseq/2.1.2/| nf-core ATAC-seq peak-calling and QC analysis pipeline]]
+
+* This is our recommendation: 
+    *  keep duplicated reads but using macs2 "--keep-dup auto". 
+    *  use --shift -75 and --extsize 150 instead of BAMPE (we want to make the highest point of the read profile around the cutting sites, not in the center of the fragment)
+* This is an example command to implement those changes with a configuration file, "macs2Custom.config". 
+{{{
+sbatch --partition=20 --job-name=NextF_ATACmcas2ConfigFull --output=NextF_ATAC_macs2ConfigFull-%j.out  --mem=200gb   --nodes=1 --ntasks=1 --cpus-per-task=20 --wrap \
+ "nextflow run nf-core/atacseq    -profile singularity  -c  ./macs2Custom.config --input ./atacseq_sampleSheetFullFastq.csv  --min_trimmed_reads  0  --aligner bowtie2  --keep_dups TRUE  --narrow_peak TRUE  --email 'username@wi.mit.edu' --genome  mm10 --read_length 50  --outdir  ./OutNextF_ATAC"
+}}}
+
+* This is the content of the config file "macs2Custom.config".
+
+{{{
+process {
+    withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:MACS2_CALLPEAK' {
+        ext.args   = [
+            '--keep-dup auto',
+            '--nomodel',
+            '--shift -75',
+            '--extsize 150',
+            '--format BAM',
+            '--bdg ',
+            '--qvalue 0.01'
+        ].join(' ').trim()
+
+    }
+}
+}}}
+
+For specific parameters of the nf-core ATAC-seq pipeline it is best to check the documentation in this page:
+* [[https://nf-co.re/atacseq/2.1.2/parameters/| nf-core ATAC-seq parameters]]
+
 === Further reading ===