From a37597db0e0a2a4530baacac00d8e3c3355abaff Mon Sep 17 00:00:00 2001
From: dhmcg77 <50170476+dhmcg77@users.noreply.github.com>
Date: Wed, 1 Jun 2022 11:25:00 +0100
Subject: [PATCH] Update run_hisat2.Rd

Index pointing to Kallisto index and not HiSat2 one
---
 man/run_hisat2.Rd | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/man/run_hisat2.Rd b/man/run_hisat2.Rd
index 031d1d8..0cb5765 100755
--- a/man/run_hisat2.Rd
+++ b/man/run_hisat2.Rd
@@ -74,8 +74,7 @@ Runs the HISAT2 tool, can be used for single end and paired end reads
                         pattern = "*_R1_001.fastq$",
                         full.names = FALSE),"_"), `[[`, 1))
 
- index <- "/export/buzz1/Genome/Homo_sapiens/Ensembl/GRCH38_p7/Sequence/Transcriptome/
-           KallistoIndex/GRCh38_p7.kall"
+ index <- "/export/buzz1/Genome/Homo_sapiens/Ensembl/GRCh38.102/indexes/hisat2/Homo_sapiens.GRCh38"
 
  # Paired End example
  strandedness <- "RF"