From 7cd2b1cd3ff842d8d690a87aaba55b15ca0e2188 Mon Sep 17 00:00:00 2001
From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com>
Date: Wed, 24 Jan 2024 15:41:01 -0800
Subject: [PATCH 1/2] Fix 3 space in counts by making them tab

---
 bin/edgerNormalize.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/edgerNormalize.R b/bin/edgerNormalize.R
index bfc2a2f..254096a 100755
--- a/bin/edgerNormalize.R
+++ b/bin/edgerNormalize.R
@@ -23,6 +23,6 @@ df.rpkm <- rpkm(x,x$genes$Length, normalized.lib.sizes=F)
 df.cpm <- cpm(x)
 df.tpm = tpm3(counts, x$genes$Length)
 
-write.table(df.rpkm, file=paste0(args[2],"_featureCounts_RPKM.txt"), row.names=T, quote=F,sep="   ")
-write.table(df.cpm, file=paste0(args[2],"_featureCounts_CPM.txt"), row.names=T, quote=F,sep="   ")
-write.table(df.tpm, file=paste0(args[2],"_featureCounts_TPM.txt"), row.names=T, quote=F,sep="   ")
+write.table(df.rpkm, file=paste0(args[2], "_featureCounts_RPKM.tsv"), row.names=T, quote=F, sep="\t")
+write.table(df.cpm, file=paste0(args[2], "_featureCounts_CPM.tsv"), row.names=T, quote=F, sep="\t")
+write.table(df.tpm, file=paste0(args[2], "_featureCounts_TPM.tsv"), row.names=T, quote=F, sep="\t")

From e587b1031948ed6ee98f64fc1348f58b4771a2eb Mon Sep 17 00:00:00 2001
From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com>
Date: Wed, 24 Jan 2024 15:43:13 -0800
Subject: [PATCH 2/2] fix deseq2 normalisation by changing 3 space to tab

---
 bin/deseq2Normalize.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/deseq2Normalize.R b/bin/deseq2Normalize.R
index 5122ac0..a9c8010 100755
--- a/bin/deseq2Normalize.R
+++ b/bin/deseq2Normalize.R
@@ -19,8 +19,8 @@ cds.norm <- counts(size.factors, normalized = T)
 
 write.table(
   cds.norm,
-  file = paste0(args[2], "_featureCounts_deseq2.txt"),
+  file = paste0(args[2], "_featureCounts_deseq2.tsv"),
   row.names = T,
   quote = F,
-  sep = "   "
+  sep = "\t"
 )