From f62ea83333b998fc544a746be8a18f276babb35c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sun, 2 Oct 2022 23:29:55 +0200 Subject: [PATCH] Add back antibody to consensus paths in output description --- docs/output.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/output.md b/docs/output.md index 604310b5..b3198554 100644 --- a/docs/output.md +++ b/docs/output.md @@ -217,7 +217,7 @@ Various QC plots per sample including number of peaks, fold-change distribution,
Output files -- `/mergedLibrary/macs2//consensus` +- `/mergedLibrary/macs2//consensus//` - `*.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
Output files -- `/mergedLibrary/macs2//consensus/deseq2/` +- `/mergedLibrary/macs2//consensus//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. - - `/mergedLibrary/macs2//consensus/deseq2/sizeFactors/` + - `/mergedLibrary/macs2//consensus//sizeFactors/` - `*.txt`, `*.RData`: Files containing DESeq2 sizeFactors per sample.