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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]0308課程  (閱讀 293 次)

admin

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[資訊]0308課程
« 於: 三月 06, 2017, 12:33:34 am »
Data
https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000546
https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP001371
http://asia.ensembl.org/info/data/ftp/index.html
ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/

Command
(1) STAR: Spliced Transcripts Alignment to a Reference
     https://github.com/alexdobin/STAR

(2) HTSeq: Analysing high-throughput sequencing data with Python
http://www-huber.embl.de/HTSeq/doc/install.html

(3) samtools: Tools for manipulating next-generation sequencing data
    https://github.com/samtools
« 最後編輯時間: 三月 08, 2017, 08:03:06 pm 由 admin »
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回覆: [資訊]0308課程
« 回覆文章 #1 於: 三月 06, 2017, 08:26:50 pm »
cat Homo_sapiens.GRCh38.dna.chromosome.12.fa >> Homo_sapiens.GRCh38.dna.chromosome.6.fa
./STAR --runMode genomeGenerate --runThreadN 6 --genomeDir ./GRCh38Chr612 --genomeFastaFiles ./GRCh38.chromosome.6.fa --sjdbGTFfile ./Homo_sapiens.GRCh38.87.gtf
./STAR --runMode genomeGenerate --runThreadN 6 --genomeDir ../GRCh38 --genomeFastaFiles ../GRCh38/GRCh38.fa --sjdbGTFfile ./Homo_sapiens.GRCh38.87.gtf


./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453392_1.fastq SRR453392_2.fastq --outFileNamePrefix S392
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453393_1.fastq SRR453393_2.fastq --outFileNamePrefix S393
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453394_1.fastq SRR453394_2.fastq --outFileNamePrefix S394
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453395_1.fastq SRR453395_2.fastq --outFileNamePrefix S395
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453396_1.fastq SRR453396_2.fastq --outFileNamePrefix S396
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453397_1.fastq SRR453397_2.fastq --outFileNamePrefix S397
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453398_1.fastq SRR453398_2.fastq --outFileNamePrefix S398
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453399_1.fastq SRR453399_2.fastq --outFileNamePrefix S399
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453400_1.fastq SRR453400_2.fastq --outFileNamePrefix S400
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453401_1.fastq SRR453401_2.fastq --outFileNamePrefix S401
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453402_1.fastq SRR453402_2.fastq --outFileNamePrefix S402
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453403_1.fastq SRR453403_2.fastq --outFileNamePrefix S403
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453404_1.fastq SRR453404_2.fastq --outFileNamePrefix S404
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453405_1.fastq SRR453405_2.fastq --outFileNamePrefix S405
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453406_1.fastq SRR453406_2.fastq --outFileNamePrefix S406
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR453407_1.fastq SRR453407_2.fastq --outFileNamePrefix S407
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR643741_1.fastq SRR643741_2.fastq --outFileNamePrefix S741
./STAR --genomeDir ../GRCh38/  --runThreadN 6 --readFilesIn SRR643742_1.fastq SRR643742_2.fastq --outFileNamePrefix S742

htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S392Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S392.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S393Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S393.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S394Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S394.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S395Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S395.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S396Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S396.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S397Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S397.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S398Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S398.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S399Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S399.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S400Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S400.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S401Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S401.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S402Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S402.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S403Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S403.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S404Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S404.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S405Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S405.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S406Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S406.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S407Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S407.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S741Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S741.counts
htseq-count -m union -r pos -i gene_name -a 10 --stranded=no S742Aligned.out.sam ./Homo_sapiens.GRCh38.87.gtf > S742.counts
已記錄
 

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