From d9e3b2b40e6a6cbbfae8a74a20a375cee2deb7e8 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 21 Mar 2020 10:08:53 -0500
Subject: [PATCH] Update documentation and use GTF file.
---
README.md | 1 +
docs/index.md | 1 +
workflow/main.nf | 1 +
3 files changed, 3 insertions(+)
diff --git a/README.md b/README.md
index ec8e8c7..bdd7b7c 100644
--- a/README.md
+++ b/README.md
@@ -73,6 +73,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
9. Annotate all peaks using ChipSeeker
10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
11. Use MEME-ChIP to find motifs in original peaks
+ 12. Plot enrichment of signal around TSS
See [FLOWCHART](docs/flowchart.pdf)
diff --git a/docs/index.md b/docs/index.md
index 3b4a685..e4e3e01 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -20,6 +20,7 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste
9. Annotate all peaks using ChipSeeker
10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
11. Use MEME-ChIP to find motifs in original peaks
+ 12. Plot enrichment of signal around TSS
## Workflow Parameters
diff --git a/workflow/main.nf b/workflow/main.nf
index cb8b1e6..90f0c90 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -488,6 +488,7 @@ process plotProfile {
output:
file '*.{png,gz}' into plotProfile
+ file gtf from gtfFile
when:
--
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