From 32e2dcdd266dc4deeb986c532ff7d30af5645ba5 Mon Sep 17 00:00:00 2001
From: PoolLab <89029708+PoolLab@users.noreply.github.com>
Date: Tue, 21 Mar 2023 00:24:47 -0500
Subject: [PATCH] Update 2_Optimized _annotation_assembler.R

---
 2_Optimized _annotation_assembler.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/2_Optimized _annotation_assembler.R b/2_Optimized _annotation_assembler.R
index 8100735..f220cbb 100644
--- a/2_Optimized _annotation_assembler.R	
+++ b/2_Optimized _annotation_assembler.R	
@@ -44,7 +44,7 @@ boundary_fix = read.csv("gene_extension_candidates.csv", header=T)
 rename_genes = read.csv("rename_genes.csv", header=T)
 
 new_df = exonic_df
-rm(exonic_gtf)
+
 
 ####  1. Create premRNA genome annotation from input gtf that defines transcripts as exons ####
 ###############################################################################################
@@ -63,7 +63,7 @@ rm(exonic_gtf)
 # --include-introns mode in Cell Ranger 6 or default mode in later ierations to retrieve 
 # most of available intronic reads.
 
-transcripts_df = exonic_df[exonic_df$type == "transcript",]
+transcripts_df = new_df[new_df$type == "transcript",]
 exons_df = transcripts_df # Create new dataframe to contain premrna exons
 exons_df$type = rep("exon", nrow(exons_df)) # rename "type" from transcripts to exon