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[開學]106學年第1學期的課程看版開張了 歡迎同學問問題-20170917

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1  技術 / Ubuntu / 回覆: 如何在Ubuntu上安裝和配置Apache 於: 五月 24, 2017, 12:42:17 am
http://www.arthurtoday.com/2009/11/ubuntu-910-mysql.html
mysql
2  技術 / Ubuntu / 如何在Ubuntu上安裝和配置Apache 於: 五月 24, 2017, 12:40:40 am
http://blog.xuite.net/hcc0110/vbdir/251189863-%E5%A6%82%E4%BD%95%E5%9C%A8Ubuntu+14.04%E4%B8%8A%E5%AE%89%E8%A3%9D%E5%92%8C%E9%85%8D%E7%BD%AEApache
程式碼: [Select]
sudo apt-get install apache2
3  科技領域 / 精準醫療 / 回覆: [Tool] BWA 於: 三月 26, 2017, 06:58:48 pm
程式碼: [Select]
samtools view -b -S SLE001-bwa.sam > SLE001-bwa.bam
samtools sort SLE001-bwa.bam SLE001-bwa-sorted
samtools index  SLE001-bwa-sorted.bam
java -jar picard.jar MarkDuplicates INPUT=SLE001-bwa-sorted.bam OUTPUT=SLE001-bwa-dedup.bam METRICS_FILE=metrics.txt
4  程式語言摘要 / R / R beginning for bioinformatics 於: 三月 22, 2017, 09:21:14 am
R https://www.r-project.org
R-studio https://www.rstudio.com
Bioconductor https://bioconductor.org
5  105學年(下)課程2017Spring / 105(下)中西醫結合的大數據分析 / [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
6  程式語言摘要 / Perl / replace 於: 三月 14, 2017, 11:48:53 pm
perl -pe 's/aaa/bbb/g' file.txt

perl -pe 's/(\W+)\s+(\W+)\s+(\W+)/$1 $3 $2/' ip.txt

\d 其實就是 [0-9], "任何一個數字"
\D 其實就是 [^0-9], "任何一個非數字"
\w 其實就是 [a-zA-Z0-9_], "任何一個文數字"
\W 其實就是 [^a-zA-Z0-9_], "任何一個非文數字"
\s 其實就是 [ \t\n], "任何一個空白類字元"
\S 其實就是 [^ \t\n], "任何一個非空白類字元"
7  科技領域 / 精準醫療 / 回覆: [Tool] Bowtie 於: 二月 25, 2017, 08:24:31 pm
bowtie2-build  AF090940.fasta af090940
bowtie2 -x af090940 -1 SLE002_R1.fastq -2 SLE002_R2.fastq -S SLE002-af090940.sam
samtools view -bS SLE002-af090940.sam > SLE002-af090940.bam
samtools sort SLE002-af090940.bam SLE002-af090940.sorted
samtools index SLE002-af090940.sorted.bam
8  科技領域 / 精準醫療 / 回覆: [Tool] Bowtie 於: 二月 21, 2017, 11:21:12 pm
程式碼: [Select]
bowtie-build Homo_sapiens.GRCh38.cdna.all.fa h38cdna

bowtie /home/bioinfo/bt1h38index/h38cdna -1 D002_R1.fastq -2 D002_R2.fastq D002.map --un D002-unmapped
9  科技領域 / 精準醫療 / [Tool] Trinity Release v2.4.0 於: 二月 17, 2017, 04:03:28 pm
-uses samtools v1.3, jellyfish 2.2.6, and trimmomatic 0.36
-seqtk now used for fastq->fasta conversions
-updated compute resource monitoring routines that leverage collectl
-included utilities to examine strand-specificity of the rna-seq reads:
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Examine-Strand-Specificity
-Trinity carefully checks formatting of 'samples_file' to ensure it uses all the samples (dealing w/ non-unix text-editor formatting issues that can bundle the entire text file into what looks like a single line of text)
-Docker image updated to include salmon for abundance estimation
-refined use of bowtie2 in chrysalis clustering and various updates to improve long-read support.
10  科技領域 / 精準醫療 / 回覆: [Tool] htseq-count 於: 二月 06, 2017, 10:54:36 am
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no E826Aligned.out.sam ~/Homo_sapiens.GRCh38.84.gtf > E826.counts
11  科技領域 / 精準醫療 / 回覆: [Tool] STAR 於: 一月 22, 2017, 09:37:39 am
STAR-command-ERP007050-HLA-20170122
//
./STAR --runMode genomeGenerate --runThreadN 4 --genomeDir ./GRCh38Chr6 --genomeFastaFiles ./Homo_sapiens.GRCh38.dna.chromosome.6.fa --sjdbGTFfile ./Homo_sapiens.GRCh38.84.gtf

./STAR --genomeDir ./GRCh38Chr6/  --runThreadN 4 --readFilesIn ERR629550_1.fastq ERR629550_2.fastq --outFileNamePrefix E550 Fastx

12  科技領域 / 數位匯流 / 回覆: WNMP伺服器配置[Windows + Nginx + MySQL + phpMyAdmin] 於: 一月 18, 2017, 02:04:01 am
nginx
https://www.nginx.com/resources/wiki/start/topics/tutorials/install/
mysql
https://dev.mysql.com/get/Downloads/MySQL-5.7/mysql-5.7.17-winx64.zip
php
https://www.nginx.com/resources/wiki/start/topics/examples/phpfastcgionwindows/
Microsoft Visual C++ 2015 Redistributable
https://www.microsoft.com/en-us/download/details.aspx?id=53587
13  科技領域 / 精準醫療 / 回覆: [Tool] htseq-count 於: 一月 04, 2017, 11:17:06 am
sudo apt-get install python python-setuptools python-pip python-matplotlib cython zlib1g-dev 
sudo pip install biopython
sudo pip install pysam

https://pypi.python.org/pypi/HTSeq

14  科技領域 / 精準醫療 / [Tool] Platypus 於: 一月 03, 2017, 02:21:31 am
http://www.well.ox.ac.uk/platypus
15  技術 / Linux/Unix作業環境 / [command] rename 於: 十一月 16, 2016, 01:00:08 am
mv a.out b.out
================
sudo apt-get install krename

141003-D002-1_S2_L001_R1_001.clean.fastq => D002_R1.fastq
rename -v   's/141003-(D\d\d\d)\S+(_R[12])\S+\.fastq$/$1$2\.fastq/' *.fastq
-v verbose -n just test
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