Update analysis.

RIP-seq.Rmd

@@ -8,6 +8,7 @@ biocLite("groHMM")
 biocLite("org.Hs.eg.db")
 biocLite("edgeR")
 biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
+biocLite("BSgenome.Hsapiens.UCSC.hg19")
 biocLite("goseq")
 install.packages("ggplot2")
 install.packages("VennDiagram")
@@ -21,6 +22,7 @@ library(GenomicFeatures)
 library(ggplot2)
 library(VennDiagram)
 library(reshape)
+library(BSgenome.Hsapiens.UCSC.hg19)
 ```
 
 ## Functions
@@ -475,8 +477,14 @@ wilcox.test(MPK_enrichment[,1], MPK_enrichment[,2],paired=T)
 ```
 
 ```{r alignments Estrogen}
+MLKE_RNA1 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RNAseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RNA1/align-star-se.sh-1.0.0/MLKE_RNA1_AGTTCC_L008_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
+MLKE_RNA2 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RNAseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RNA2/align-star-se.sh-1.0.0/MLKE_RNA2_GTGAAA_L008_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
 
+MLKE_RIP_PI1 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PI/align-star-se.sh-2.0.0/MLKE_RIP1_PI_CAGATC_L006_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
+MLKE_RIP_PI2 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PI/align-star-se.sh-2.0.0/MLKE_RIP2_PI_GAGTGG_L008_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
 
+MLKE_RIP_PARP1 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PARP1_SecondRun/align-star-se.sh-2.0.0/MLKE_RIP1_PARP1_ACTTGA_L004_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
+MLKE_RIP_PARP2 <- "/Volumes/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PARP1_16/align-star-se.sh-2.0.0/MLKE_RIP2_PARP1_16_CCGTCC_L007_R1.rDNA.filtered.fastq.gz_filtered_chrMAligned.sortedByCoord.out.bam"
 ```
 
 ```{r counts Estrogen}
@@ -753,6 +761,7 @@ write.table(mlke_allsnotx_rna_rpkm, file="mcf-7-e2-snRNA_RPKM_RNA.tsv", quote=F,
 
 ```
 
+
 # Overlap of snoRNA and snRNA
 ``` {r snoRNA Overlap}