Merge pull request #309 from JoseEspinosa/updates

Add back antibody to consensus paths in output description

Author: drpatelh

docs/output.md

@@ -217,7 +217,7 @@ Various QC plots per sample including number of peaks, fold-change distribution,
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus`
+- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/`
   - `*.bed`: Consensus peak-set across all samples in BED format.
   - `*.saf`: Consensus peak-set across all samples in SAF format. Required by featureCounts for read quantification.
   - `*.featureCounts.txt`: Read counts across all samples relative to consensus peak-set.
@@ -245,7 +245,7 @@ The [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) tool is used to co
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/deseq2/`
+- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/deseq2/`
   - `*.sample.dists.txt`: Spreadsheet containing sample-to-sample distance across each consensus peak.
   - `*.plots.pdf`: File containing PCA and hierarchical clustering plots.
   - `*.dds.RData`: File containing R `DESeqDataSet` object generated by DESeq2, with either
@@ -254,7 +254,7 @@ The [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) tool is used to co
     `readRDS` to give user control of the eventual object name.
   - `*pca.vals.txt`: Matrix of values for the first 2 principal components.
   - `R_sessionInfo.log`: File containing information about R, the OS and attached or loaded packages.
-  - `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/deseq2/sizeFactors/`
+  - `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/sizeFactors/`
   - `*.txt`, `*.RData`: Files containing DESeq2 sizeFactors per sample.
 
 </details>