# HG changeset patch
# User saharlcc
# Date 1496589045 14400
# Node ID b07d4238ba9bcad9afa12c18b02dab4b9a0d351c
# Parent  ab5e4602bd28a9e475b1940b22a9cf2028017ad2
Updating README

diff -r ab5e4602bd28 -r b07d4238ba9b isoem2_isode2/README.txt
--- a/isoem2_isode2/README.txt	Fri May 26 10:45:35 2017 -0400
+++ b/isoem2_isode2/README.txt	Sun Jun 04 11:10:45 2017 -0400
@@ -5,8 +5,6 @@
 2) Download and install  IsoEM2/IsoDE2 (https://github.com/mandricigor/isoem2)
 
 3) Install other dependencies:
-- tmap (needed for ION Torrent data)
-  Available at https://github.com/iontorrent/TMAP
 - hisat2 (needed for Illumina data) 
   Available at https://ccb.jhu.edu/software/hisat2/index.shtml
 - prinseq 
@@ -16,11 +14,14 @@
 
 4) Edit isoem_wrapper.sh and IsoDE2.sh. Change tool paths to where they are installed on your system 
 
-5) build hisat2 for the reference you will use for mapping
+5) Copy .loc file under tool-data directory in Galaxy
+
+6) build hisat2 for the reference you will use for mapping
 
-6) Edit the .loc file with paths to your reference files: GTF, Transcript to gene cluster, and mapper indices), and copy it under tool-data directory in Galaxy
-Note: If you need only one of the two mappers (say hisat2), you can replace the other path to the other maaper index with a dummy path
+7) Edit the .loc file with paths to your reference files: GTF, Transcript to gene cluster, and mapper index).
 
-7) copy the entry in the tool_data_table_conf.xml file provided in this repository to the tool_data_table_conf.xml in your Galaxy config directory
+Note: steps 6 and 7 are not needed if you will use IsoEM2 option "Use reference from the history" and not "Use a built-in reference"
+
+8) copy the entry in the tool_data_table_conf.xml file provided in this repository to the tool_data_table_conf.xml in your Galaxy config directory