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Update RNA-Seq Coverage.ipynb #2

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109 changes: 29 additions & 80 deletions RNA-Seq Coverage/RNA-Seq Coverage.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,7 @@
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand All @@ -62,9 +60,7 @@
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -100,9 +96,7 @@
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [],
"source": [
"using Bio.Align"
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@CiaranOMara CiaranOMara Jan 5, 2020

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The current package is BioAlignments v1.

Expand All @@ -111,9 +105,7 @@
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -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\")"
]
},
{
Expand All @@ -143,9 +135,7 @@
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -184,9 +174,7 @@
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -216,9 +204,7 @@
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -238,9 +224,7 @@
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand All @@ -265,7 +249,6 @@
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [
Expand Down Expand Up @@ -309,9 +292,7 @@
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -331,9 +312,7 @@
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -372,9 +351,7 @@
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -401,9 +378,7 @@
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -430,9 +405,7 @@
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [],
"source": [
"# count the number of mapped records\n",
Expand Down Expand Up @@ -479,9 +452,7 @@
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -508,9 +479,7 @@
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -673,9 +642,7 @@
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -712,9 +679,7 @@
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -758,9 +723,7 @@
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -788,9 +751,7 @@
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -850,9 +811,7 @@
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -899,9 +858,7 @@
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -924,9 +881,7 @@
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [],
"source": [
"chr2_mrna = readlines(pl);"
Expand All @@ -942,9 +897,7 @@
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"data": {
Expand All @@ -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",
Expand All @@ -983,9 +934,7 @@
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand All @@ -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,
Expand Down