3. Map reads with BWA, filter with SamTools, and sort with Sambamba
4. Mark duplicates with Sambamba, Filter reads with SamTools, calculate percentage of reads in mitochondria, and calculate library complexity with SamTools and bedtools
5. Calculate cross-correlation using PhantomPeakQualTools
6. Call peaks with MACS2 from overlaps of pooled replicates
7. Call consensus peaks
7. Call consensus peaks and optional removal of blacklist peaks
8. QC metrics
9. MultiQC report
...
...
@@ -79,6 +79,7 @@ callPeaksMACS | pooled/*.pvalue_signal.bw | bigwig data file; sample/control sig
callPeaksMACS | pooled/*_pooled.narrowPeak | peaks file; see [HERE](https://genome.ucsc.edu/FAQ/FAQformat.html#format12) for ENCODE narrowPeak header format
consensusPeaks | *.rejected.narrowPeak | peaks not supported by multiple testing (replicates and pseudo-replicates)
consensusPeaks | *.replicated.narrowPeak | peaks supported by multiple testing (replicates and pseudo-replicates)
consensusPeaks | *.replicated_noblacklist.narrowPeak | peaks supported by multiple testing (replicates and pseudo-replicates) with blacklist regions removed
experimentQC | coverage.pdf | plot to assess the sequencing depth of a given sample
experimentQC | heatmeap_SpearmanCorr.pdf | plot of Spearman correlation between samples
experimentQC | heatmeap_PearsonCorr.pdf | plot of Pearson correlation between samples
3. Map reads with BWA, filter with SamTools, and sort with Sambamba
4. Mark duplicates with Sambamba, Filter reads with SamTools, calculate percentage of reads in mitochondria, and calculate library complexity with SamTools and bedtools
5. Calculate cross-correlation using PhantomPeakQualTools
6. Call peaks with MACS2 from overlaps of pooled replicates
7. Call consensus peaks
7. Call consensus peaks and optional removal of blacklist peaks
8. QC metrics
9. MultiQC report
...
...
@@ -79,6 +79,7 @@ callPeaksMACS | pooled/*.pvalue_signal.bw | bigwig data file; sample/control sig
callPeaksMACS | pooled/*_pooled.narrowPeak | peaks file; see [HERE](https://genome.ucsc.edu/FAQ/FAQformat.html#format12) for ENCODE narrowPeak header format
consensusPeaks | *.rejected.narrowPeak | peaks not supported by multiple testing (replicates and pseudo-replicates)
consensusPeaks | *.replicated.narrowPeak | peaks supported by multiple testing (replicates and pseudo-replicates)
consensusPeaks | *.replicated_noblacklist.narrowPeak | peaks supported by multiple testing (replicates and pseudo-replicates) with blacklist regions removed
experimentQC | coverage.pdf | plot to assess the sequencing depth of a given sample
experimentQC | heatmeap_SpearmanCorr.pdf | plot of Spearman correlation between samples
experimentQC | heatmeap_PearsonCorr.pdf | plot of Pearson correlation between samples