Alternative splicing, splice variant, isoformを検出、定量、比較する。
段取りとしてはFASTQのQC→トリミング→マッピング→AS analysis (& visualization)
QC,トリミング,マッピングまではこれまでにやってきた組み合わせでいいはず。
cufflinksで発現量比較をする代わりにASを検出するソフトウェアにかける。
試してみるソフト
MISO(334) http://genes.mit.edu/burgelab/miso/
featureCounts(346)/DEXSeq http://subread.sourceforge.net http://bioconductor.org/packages/release/bioc/html/DEXSeq.html
rMATS(46) http://rnaseq-mats.sourceforge.net
VAST-TOOLS(48) https://github.com/vastgroup/vast-tools
（）内はPubMedでの被引用回数。上2つがよく使われている様子。ただし引用はソフトウェアについてとは限らない。
MISO, rMATSインストール
python2.7以上必要。→python3入ってる
NumPy, SciPy, pysamをインストールしておく
$ pip3 install Numpy
Collecting Numpy
Downloading numpy-1.13.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.5MB)
100% | 4.5MB 346kB/s
Installing collected packages: Numpy
Successfully installed Numpy-1.13.0
$ pip3 install SciPy
Collecting SciPy
Downloading scipy-0.19.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.2MB)
100% | 16.2MB 90kB/s
Requirement already satisfied: numpy>=1.8.2 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from SciPy)
Installing collected packages: SciPy
Successfully installed SciPy-0.19.1
$ pip3 install pysam
Collecting pysam
Downloading pysam-0.11.2.2.tar.gz (2.5MB)
100% | 2.5MB 605kB/s
Installing collected packages: pysam
Running setup.py install for pysam ... done
Successfully installed pysam-0.11.2.2
$ pip3 install matplotlib
Collecting matplotlib
Downloading matplotlib-2.0.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (12.8MB)
100% | 12.8MB 115kB/s
Collecting python-dateutil (from matplotlib)
Downloading python_dateutil-2.6.0-py2.py3-none-any.whl (194kB)
100% | 194kB 6.4MB/s
Collecting cycler>=0.10 (from matplotlib)
Downloading cycler-0.10.0-py2.py3-none-any.whl
Collecting six>=1.10 (from matplotlib)
Downloading six-1.10.0-py2.py3-none-any.whl
Requirement already satisfied: numpy>=1.7.1 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib)
Collecting pytz (from matplotlib)
Downloading pytz-2017.2-py2.py3-none-any.whl (484kB)
100% | 491kB 3.2MB/s
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib)
Downloading pyparsing-2.2.0-py2.py3-none-any.whl (56kB)
100% | 61kB 11.3MB/s
Installing collected packages: six, python-dateutil, cycler, pytz, pyparsing, matplotlib
Successfully installed cycler-0.10.0 matplotlib-2.0.2 pyparsing-2.2.0 python-dateutil-2.6.0 pytz-2017.2 six-1.10.0
SAMtools(1.2以上）が必要→ある(v1.4.1)
STARが必要→バイナリをダウンロードしておく https://github.com/alexdobin/STAR
必要なものが揃ったようなのでMISOのサイトの言われるままに
$ pip3 install misopy
Collecting misopy
Downloading misopy-0.5.3.tar.gz (1.5MB)
100% | 1.5MB 972kB/s
Requirement already satisfied: matplotlib in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from misopy)
Requirement already satisfied: numpy>=1.5.0 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from misopy)
Requirement already satisfied: scipy>=0.9.0 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from misopy)
Requirement already satisfied: pysam>=0.6.0 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from misopy)
Requirement already satisfied: pytz in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib->misopy)
Requirement already satisfied: cycler>=0.10 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib->misopy)
Requirement already satisfied: six>=1.10 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib->misopy)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib->misopy)
Requirement already satisfied: python-dateutil in /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages (from matplotlib->misopy)
Installing collected packages: misopy
Running setup.py install for misopy ... errorこのあと盛大にエラーメッセージが流れ
$ pip3 list --format=legacy cycler (0.10.0) matplotlib (2.0.2) numpy (1.13.0) pip (9.0.1) pyparsing (2.2.0) pysam (0.11.2.2) python-dateutil (2.6.0) pytz (2017.2) scipy (0.19.1) setuptools (28.8.0) six (1.10.0)
やはりインストールされていない。
pythonのバージョンが３だと新しすぎるのか？
osxに元から入っているpython2.7を使えばいい気はするが、2.7のpipって入ってないし。
