Resolve "Blacklist of regions"

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• This comment contains a description of changes (with reason)
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Closes #31 (closed)

docs/index.md

@@ -43,14 +43,14 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
 
 
 ## Pipeline
-  + There are ??? steps to the pipeline
+  + There are 9 steps to the pipeline
     1. Check input files
     2. Trim adaptors with TrimGalore!
     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