wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP064%2FSRP064411/SRR2549634/SRR2549634.sra
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP064%2FSRP064411/SRR2549635/SRR2549635.sra
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP064%2FSRP064411/SRR2549636/SRR2549636.sra
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP064%2FSRP064411/SRR2549637/SRR2549637.sra
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP064%2FSRP064411/SRR2549638/SRR2549638.sra
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP064%2FSRP064411/SRR2549639/SRR2549639.sra
fastq-dump -I --split-files SRR2549634.sra
fastq-dump -I --split-files SRR2549636.sra
fastq-dump -I --split-files SRR2549638.sra
fastq-dump -I --split-files SRR2549635.sra
fastq-dump -I --split-files SRR2549637.sra
fastq-dump -I --split-files SRR2549639.sra
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae_Ensembl_R64-1-1.tar.gz
gzip -d Saccharomyces_cerevisiae_Ensembl_R64-1-1.tar.gz
tar xvf Saccharomyces_cerevisiae_Ensembl_R64-1-1.tar
bowtie2 -x Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome -U SRR2549634_1.fastq -S SRR2549634_1.sam
bowtie2 -x Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome -U SRR2549636_1.fastq -S SRR2549636_1.sam
bowtie2 -x Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome -U SRR2549638_1.fastq -S SRR2549638_1.sam
bowtie2 -x Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome -U SRR2549635_1.fastq -S SRR2549635_1.sam
bowtie2 -x Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome -U SRR2549637_1.fastq -S SRR2549637_1.sam
bowtie2 -x Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/genome -U SRR2549639_1.fastq -S SRR2549639_1.sam
samtools view -bS SRR2549634_1.sam | samtools sort - SRR2549634_1
samtools view -bS SRR2549636_1.sam | samtools sort - SRR2549636_1
samtools view -bS SRR2549638_1.sam | samtools sort - SRR2549638_1
samtools view -bS SRR2549635_1.sam | samtools sort - SRR2549635_1
samtools view -bS SRR2549637_1.sam | samtools sort - SRR2549637_1
samtools view -bS SRR2549639_1.sam | samtools sort - SRR2549639_1
SRR2549634_1.bam
SRR2549636_1.bam
SRR2549638_1.bam
SRR2549635_1.bam
SRR2549637_1.bam
SRR2549639_1.bam
It can be done with
ls *.bam > bamfiles.txt
library(Rsamtools)
library(GenomicFeatures)
= read.table("bamfiles.txt")
sampleTable = paste(getwd(),"/",sep="")
dirActualData = paste(dirActualData,sampleTable[,1],sep="")
fls = BamFileList(fls, index=character(),yieldSize=100000,obeyQname=TRUE)
bamLst = "../Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
gtfFile = makeTxDbFromGFF(gtfFile, format="gtf")
txdb = exonsBy(txdb, by="gene")
genes library(GenomicAlignments)
= summarizeOverlaps(features = genes, read=bamLst,
PRJNA297664 mode="Union",
singleEnd=TRUE, ## No son lecturas apareadas
ignore.strand=TRUE,
fragments=FALSE)
= c("GSM1900735","GSM1900737","GSM1900739","GSM1900736",
SampleName "GSM1900738","GSM1900740")
= c("SRR2549634","SRR2549636","SRR2549638","SRR2549635",
Run "SRR2549637","SRR2549639")
= c(0,0,1,0,1,1)
treatment = factor(treatment,levels=0:1,labels=c("Wild","SEC66 deletion"))
treatment = c(1,3,2,2,1,3)
replication colData(PRJNA297664) = DataFrame(SampleName,Run,treatment,replication)
= AnnotationDbi::select(org.Sc.sgd.db,keys=rownames(PRJNA297664),
a columns=c("ORF","ENTREZID","ENSEMBL"),keytype="ORF")
= match(rownames(PRJNA297664),a[,"ORF"])
b rowData(PRJNA297664) = a[b,]
= PRJNA297664[which(!is.na(rowData(PRJNA297664)[,"ORF"])),]
PRJNA297664 = match(unique(rowData(PRJNA297664)[,"ORF"]),rowData(PRJNA297664)[,"ORF"])
sel = PRJNA297664[sel,] PRJNA297664
save(PRJNA297664,file="PRJNA297664.rda")