diff --git a/RNA-Seq Coverage/RNA-Seq Coverage.ipynb b/RNA-Seq Coverage/RNA-Seq Coverage.ipynb
index 55d9094..a69b2b7 100644
--- a/RNA-Seq Coverage/RNA-Seq Coverage.ipynb	
+++ b/RNA-Seq Coverage/RNA-Seq Coverage.ipynb	
@@ -38,9 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -62,9 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -100,9 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "using Bio.Align"
@@ -111,9 +105,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -130,7 +122,7 @@
    ],
    "source": [
     "bamfile = \"SRR1238088/SRR1238088.sort.bam\"\n",
-    "reader = open(BAMReader, bamfile, index=bamfile * \".bai\")"
+    "reader = open(BAM.Reader, bamfile, index=bamfile * \".bai\")"
    ]
   },
   {
@@ -143,9 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -184,9 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -216,9 +204,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -238,9 +224,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -265,7 +249,6 @@
    "cell_type": "code",
    "execution_count": 9,
    "metadata": {
-    "collapsed": false,
     "scrolled": false
    },
    "outputs": [
@@ -309,9 +292,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -331,9 +312,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -372,9 +351,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -401,9 +378,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -430,9 +405,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# count the number of mapped records\n",
@@ -479,9 +452,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -508,9 +479,7 @@
   {
    "cell_type": "code",
    "execution_count": 16,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -673,9 +642,7 @@
   {
    "cell_type": "code",
    "execution_count": 17,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -712,9 +679,7 @@
   {
    "cell_type": "code",
    "execution_count": 18,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -758,9 +723,7 @@
   {
    "cell_type": "code",
    "execution_count": 19,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -788,9 +751,7 @@
   {
    "cell_type": "code",
    "execution_count": 20,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -850,9 +811,7 @@
   {
    "cell_type": "code",
    "execution_count": 21,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -899,9 +858,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -924,9 +881,7 @@
   {
    "cell_type": "code",
    "execution_count": 23,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "chr2_mrna = readlines(pl);"
@@ -942,9 +897,7 @@
   {
    "cell_type": "code",
    "execution_count": 24,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -971,9 +924,7 @@
   {
    "cell_type": "code",
    "execution_count": 25,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# ProgressMeter.jl is useful for long-running analysis.\n",
@@ -983,9 +934,7 @@
   {
    "cell_type": "code",
    "execution_count": 26,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -1007,15 +956,15 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 0.5.0-rc4",
+   "display_name": "Julia 1.1.1",
    "language": "julia",
-   "name": "julia-0.5"
+   "name": "julia-1.1"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "0.5.0"
+   "version": "1.1.1"
   }
  },
  "nbformat": 4,