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[慶賀]恭喜張清貿醫師升任北榮傳醫科主治醫師-20170201

作者 主題: [資訊]0315課程  (閱讀 261 次)

ngstool

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[資訊]0315課程
« 於: 三月 15, 2017, 04:44:27 pm »
STAR
https://github.com/alexdobin/STAR
------------------------------------------------------------
HTSeq
http://www-huber.embl.de/HTSeq/doc/install.html
============================================================
程式碼: [Select]
./STAR --genomeDir ../GRCh38/  --runThreadN 4 --readFilesIn SRR980479_1.fastq SRR980479_2.fastq --outFileNamePrefix S479
Mar 15 12:31:30 ..... started STAR run
Mar 15 12:31:30 ..... loading genome
Mar 15 12:45:10 ..... started mapping
Mar 15 12:45:42 ..... finished successfully

HTSeq
(1) Make sure that the standard GNU build environment installed. Users of Ubuntu Linux simply type:
程式碼: [Select]
sudo apt-get install build-essential python2.7-dev python-numpy python-matplotlib
(2) Install HTSeq. Download the source package from https://pypi.python.org/pypi/HTSeq, unpack the tarball, go into the directory with the unpacked files and type there
程式碼: [Select]
python setup.py build
sudo python setup.py install

(3) Run the command
程式碼: [Select]
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S479Aligned.out.sam ../Homo_sapiens.GRCh38.87.gtf > S479.counts
« 最後編輯時間: 四月 21, 2017, 09:34:46 am 由 admin »
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