diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 11758718b03b0f334e4104251194cf0bf976511b..3943225353d510c17aed04324529aa70099979b4 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -670,7 +670,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 232,
+   "execution_count": 239,
    "metadata": {
     "collapsed": false
    },
@@ -683,7 +683,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 233,
+   "execution_count": 240,
    "metadata": {
     "collapsed": false
    },
@@ -716,11 +716,13 @@
     "    print(matches.readline())\n",
     "    print(matches.readline())\n",
     "    print(matches.readline())\n",
-    "        \n",
+    "    \n",
     "    # Generator over fastq where the corresponding sam field is 4,\n",
     "    # meaning no reported alignment\n",
-    "    sub_iter = (rec for rec in filt_iter \\\n",
-    "                if matches.readline().split('\\t')[1] == '4')\n",
+    "    #sub_iter = (rec for rec in filt_iter \\\n",
+    "    #            if matches.readline().split('\\t')[1] == '4')\n",
+    "    \n",
+    "    \n",
     "\n",
     "    # Write back fastq\n",
     "    SeqIO.write(sub_iter,substracted,\"fastq\")"
@@ -728,19 +730,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 234,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Filtering non-codant tRNA run time : 0:00:01.407564\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Store current time\n",
     "after = datetime.datetime.now()\n",
@@ -751,40 +745,6 @@
     "print(\"Filtering non-codant tRNA run time : {0}\".format(delta))"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "# Testing\n",
-    "\n",
-    "with open(\"3-Filtered/\"     +fname+\".fastq\",\"r\") as filtered, \\\n",
-    "     open(\"4-Bowtied/\"      +fname+\".sam\",\"r\")   as matches,  \\\n",
-    "     open(\"5-ncRNA-Removed/\"+fname+\".fastq\",\"w\") as substracted: \n",
-    "    \n",
-    "    # Iterator over fastq file\n",
-    "    filt_iter = SeqIO.parse(filtered,\"fastq\")\n",
-    "    \n",
-    "    # Strip header (as in original script)\n",
-    "    for _ in range(415-3): matches.readline()\n",
-    "\n",
-    "    # Check last lines\n",
-    "    print(matches.readline())\n",
-    "    print(matches.readline())\n",
-    "    print(matches.readline())\n",
-    "        \n",
-    "    # Generator over fastq where the corresponding sam field is 4,\n",
-    "    # meaning no reported alignment\n",
-    "    sub_iter = (rec for rec in filt_iter \\\n",
-    "                if matches.readline().split('\\t')[1] == '4')\n",
-    "\n",
-    "    # Write back fastq\n",
-    "    SeqIO.write(sub_iter,substracted,\"fastq\")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -796,27 +756,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 235,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Time loading forward index: 00:00:00\n",
-      "Time loading mirror index: 00:00:00\n",
-      "End-to-end 2/3-mismatch full-index search: 00:00:00\n",
-      "# reads processed: 445\n",
-      "# reads with at least one reported alignment: 240 (53.93%)\n",
-      "# reads that failed to align: 205 (46.07%)\n",
-      "Reported 240 alignments to 1 output stream(s)\n",
-      "Time searching: 00:00:00\n",
-      "Overall time: 00:00:00\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%bash\n",
     "source ./source\n",
@@ -841,7 +785,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 236,
+   "execution_count": null,
    "metadata": {
     "collapsed": true
    },
@@ -872,7 +816,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 237,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
@@ -916,7 +860,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 238,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },