Adding demo.

mozack · May 2, 2016 · fb5ff47 · fb5ff47
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diff --git a/demo/demo.bash b/demo/demo.bash
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+#!/bin/bash
+#
+# Demo script for V'DJer
+
+# Before running this script:
+# Run make to generate the vdjer executable.
+# Download the vdjer references and untar, updating the VDJER_REF_DIR variable below.
+
+VDJER_REF_DIR=<path/to/vdjer/referenes>/igh
+
+VDJER=../vdjer
+
+# Run V'DJer on the input BAM file for the IgH chain.
+# read length = 50
+# median insert size = 175
+# num threads = 4
+# 
+# Assembled contigs appear in vdj_contigs.fa
+# Reads mapped to contigs appear in vdjer.sam
+$VDJER --in star.sort.bam --rl 50 --t 4 --ins 175 --chain IGH --ref-dir $VDJER_REF_DIR > vdjer.sam 2> vdjer.log
diff --git a/demo/star.sort.bam b/demo/star.sort.bam
diff --git a/demo/star.sort.bam.bai b/demo/star.sort.bam.bai