Resolve "Annotate peaks"

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• This comment contains a description of changes (with reason)
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• Documentation in docs is updated
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Closes #32 (closed)

docs/index.md

@@ -43,7 +43,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
 
 
 ## Pipeline
-  + There are 9 steps to the pipeline
+  + There are 10 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
@@ -51,8 +51,9 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
     5. Calculate cross-correlation using PhantomPeakQualTools
     6. Call peaks with MACS2 from overlaps of pooled replicates
     7. Call consensus peaks and optional removal of blacklist peaks
-    8. QC metrics
-    9. MultiQC report
+    8. Annotate peaks (chr only; either blacklist removed or replicated)
+    9. QC metrics
+    10. MultiQC report
 
 
 ## Output Files
@@ -80,6 +81,9 @@ callPeaksMACS | pooled/*_pooled.narrowPeak | peaks file; see [HERE](https://geno
 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
+peakAnnotation | *.chipseeker_annotation.tsv | annotation of chromosomal peaks of either blacklist removed or replicated peaks
+peakAnnotation | *.chipseeker_upsetplot.pdf | upsetplot showing the count of overlaps of the genes with different annotated location
+peakAnnotation | *.chipseeker_pie.pdf | pie graph of where narrow annotated peaks occur
 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