/
BiGo_dev.ipynb
executable file
·8444 lines (8444 loc) · 276 KB
/
BiGo_dev.ipynb
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{
"metadata": {
"name": "",
"signature": "sha256:d25d8311f265ef9ddeed504218561f8650952232ceb91bba374035ab7e9934e4"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## IPython Notebook for downloading and analyzing data for the manusript: \"Indication of family-specific DNA methylation patterns in developing oysters\"\n",
"\n",
"bioRix preprint - [http://dx.doi.org/10.1101/012831](http://dx.doi.org/10.1101/012831)\n",
"\n",
"---\n",
"To execute the IPython Notebook in its entirety you will need: \n",
"\n",
"* IPython - [install instructions](http://ipython.org/install.html) \n",
"* BSMAP - [install instructions](https://code.google.com/p/bsmap/) \n",
"* bedtools - [install instructions](https://github.com/arq5x/bedtools2/releases/tag/v2.22.0) \n",
"* R - [install instructions](http://www.r-project.org/) \n",
"* rpy2 (interface to R from Python) - [install instructions](http://rpy.sourceforge.net/) \n",
"\n",
"\n",
"---\n",
"\n",
"Sofware versions originally used in this analyses (on Mac OS X v10.7.5) are as follows: \n",
"\n",
"* IPython: 2.3.0 \n",
"* BSMAP: 2.74 \n",
"* bedtools: 2.17.0 \n",
"* R: 3.1.1 \n",
"* rpy2: 2.5.0 "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"The intent is to download the github repository locally and run so accompaning scripts, etc. are available.\n",
"Detailed Instructions are provided in [GitHub Repo Readme](https://github.com/che625/olson-ms-nb).\n",
"Please note Data files that you will download and will produce are large (>20Gb).\n",
"\n",
"\n",
"The notebook is divided into 5 sections \n",
"\n",
"* [Downloading data](#Downloading-Files) \n",
"\n",
"* [Read aligning: BSMAP](#Running-BSMAP) \n",
"\n",
"* [Global differences: methylkit](#Global-Differences:-methylkit) \n",
"\n",
"* [Differentially methylated loci: methylkit](#Differentially-methylated-loci) \n",
"\n",
"* [Genomic location of DMLs: bedtools](#Genomic-location-of-DMLs) \n",
"\n",
"\n",
"Please post any comments and questions in [issues](https://github.com/che625/olson-ms-nb/issues).\n",
"\n",
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Before getting started, set the location of BSMAP on your computer and hit shift-enter"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"bsmaploc=\"/Users/Shared/Apps/bsmap-2.74/\""
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Downloading Data"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#to confirm you current directory run the command and you should see a wd directory\n",
"!ls\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\u001b[31mBiGo_dev.ipynb\u001b[m\u001b[m README.md \u001b[34mscripts\u001b[m\u001b[m \u001b[34mwd\u001b[m\u001b[m\r\n"
]
}
],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd wd"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Users/sr320/git-repos/olson-ms-nb/wd\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#This command downloads a archived file including six BS-seq libraries (4.3 Gb)\n",
"\n",
"#!wget http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_HTSdata/BiGo_lar_fastq_mcf.tgz\n",
"!curl -O http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_HTSdata/BiGo_lar_fastq_mcf.tgz \n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\r\n",
" Dload Upload Total Spent Left Speed\r\n",
"\r",
" 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0"
]
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"\r",
" 55 4221M 55 2341M 0 0 53.6M 0 0:01:18 0:00:43 0:00:35 62.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 56 4221M 56 2400M 0 0 53.7M 0 0:01:18 0:00:44 0:00:34 62.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 58 4221M 58 2474M 0 0 54.1M 0 0:01:17 0:00:45 0:00:32 66.2M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 59 4221M 59 2528M 0 0 54.1M 0 0:01:18 0:00:46 0:00:32 61.3M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 61 4221M 61 2605M 0 0 54.6M 0 0:01:17 0:00:47 0:00:30 65.1M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 62 4221M 62 2639M 0 0 54.2M 0 0:01:17 0:00:48 0:00:29 59.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 64 4221M 64 2712M 0 0 54.6M 0 0:01:17 0:00:49 0:00:28 62.5M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 66 4221M 66 2786M 0 0 54.9M 0 0:01:16 0:00:50 0:00:26 62.5M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 67 4221M 67 2862M 0 0 55.3M 0 0:01:16 0:00:51 0:00:25 67.6M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 69 4221M 69 2944M 0 0 55.9M 0 0:01:15 0:00:52 0:00:23 67.8M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 71 4221M 71 3028M 0 0 56.4M 0 0:01:14 0:00:53 0:00:21 77.5M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 72 4221M 72 3079M 0 0 56.3M 0 0:01:14 0:00:54 0:00:20 73.3M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 74 4221M 74 3145M 0 0 56.5M 0 0:01:14 0:00:55 0:00:19 71.8M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 76 4221M 76 3239M 0 0 57.1M 0 0:01:13 0:00:56 0:00:17 75.4M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 78 4221M 78 3319M 0 0 57.5M 0 0:01:13 0:00:57 0:00:16 74.6M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 79 4221M 79 3370M 0 0 57.4M 0 0:01:13 0:00:58 0:00:15 68.5M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 82 4221M 82 3466M 0 0 58.0M 0 0:01:12 0:00:59 0:00:13 77.3M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 84 4221M 84 3557M 0 0 58.6M 0 0:01:11 0:01:00 0:00:11 82.4M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 86 4221M 86 3650M 0 0 59.1M 0 0:01:11 0:01:01 0:00:10 82.0M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 88 4221M 88 3727M 0 0 59.4M 0 0:01:10 0:01:02 0:00:08 81.8M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 89 4221M 89 3790M 0 0 59.5M 0 0:01:10 0:01:03 0:00:07 84.0M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 92 4221M 92 3885M 0 0 60.0M 0 0:01:10 0:01:04 0:00:06 83.9M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 94 4221M 94 3981M 0 0 60.6M 0 0:01:09 0:01:05 0:00:04 84.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 96 4221M 96 4078M 0 0 61.1M 0 0:01:09 0:01:06 0:00:03 85.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 98 4221M 98 4175M 0 0 61.6M 0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 0:01:08 0:01:07 0:00:01 89.5M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 99 4221M 99 4216M 0 0 61.3M 0 0:01:08 0:01:08 --:--:-- 85.1M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 4221M 100 4221M 0 0 61.3M 0 0:01:08 0:01:08 --:--:-- 82.1M\r\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#uncompress files\n",
"!tar -zxvf BiGo_lar_fastq_mcf.tgz"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"x mcf_M1_R1.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_M1_R2.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_M3_R1.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_M3_R2.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T1D3_R1.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T1D3_R2.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T1D5_R1.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T1D5_R2.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T3D3_R1.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T3D3_R2.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T3D5_R1.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"x mcf_T3D5_R2.fastq"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#remove BiGo_lar_fastq_mcf.tgz\n",
"#!rm BiGo_lar_fastq_mcf.tgz "
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Downloading the oyster genome \n",
"#!wget http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa\n",
"!curl -O http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \n",
" "
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\r\n",
" Dload Upload Total Spent Left Speed\r\n",
"\r",
" 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 11 541M 11 64.0M 0 0 65.1M 0 0:00:08 --:--:-- 0:00:08 65.2M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 23 541M 23 126M 0 0 64.0M 0 0:00:08 0:00:01 0:00:07 64.1M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 38 541M 38 206M 0 0 69.0M 0 0:00:07 0:00:02 0:00:05 69.0M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 51 541M 51 280M 0 0 70.5M 0 0:00:07 0:00:03 0:00:04 70.6M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 63 541M 63 342M 0 0 68.7M 0 0:00:07 0:00:04 0:00:03 68.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 78 541M 78 424M 0 0 70.8M 0 0:00:07 0:00:05 0:00:02 71.9M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
" 92 541M 92 500M 0 0 71.7M 0 0:00:07 0:00:06 0:00:01 74.7M"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 541M 100 541M 0 0 71.5M 0 0:00:07 0:00:07 --:--:-- 73.1M\r\n"
]
}
],
"prompt_number": 5
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Running BSMAP"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"for i in (\"M1\",\"T1D3\",\"T1D5\", \"M3\", \"T3D3\", \"T3D5\"):\n",
" !{bsmaploc}bsmap \\\n",
"-a mcf_{i}_R1.fastq \\\n",
"-b mcf_{i}_R2.fastq \\\n",
"-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n",
"-o bsmap_out_{i}.sam \\\n",
"-p 8"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"BSMAP v2.74\r\n",
"Start at: Tue Dec 2 14:03:03 2014\r\n",
"\r\n",
"Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" \t(format: FASTA)\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Load in 7658 db seqs, total size 557717710 bp. 9 secs passed\r\n",
"total_kmers: 43046721\r\n"
]