head(dfLE,2) # gene_symbol Chrom Strand LEstart TES ‘LEstart’ means the start genomic position of last 3’ exon. Means closest 3’ splice site: head(dfIPA,2) # PASid gene_symbol Chrom Strand Pos upstreamSS downstreamSS Means the closest 5’ or 3’ splice site to IPA, ‘downstreamSS’ # 2 Lypla1 chr1 + 4835237 4836816 4835097ĭfIPA is a data frame containing 8 columns for Intronic PASs ‘upstreamSS’ The refUTRraw is a data frame containingĦ columns for genomic information of 3’UTR PASs: head(refUTRraw,2) # gene_symbol Chrom Strand First Last cdsend This extdata covers 3’UTR APA regions (refUTRraw), IPA regions (dfIPA),Īnd 3’-most exon regions (dfLE). Source_data(paste0(URL,file,"?raw=True")) # Downloading data from: # SHA-1 hash of the downloaded data file is: Which can be loaded from extdata: library(repmis) We have pre-built a reference file for the mouse genome (mm9), PAS references in the genome (both 3’UTRs and introns) are required by our suppressMessages(library("TBX20BamSubset")) In this example,īAM files correspond to mouse RNA-seq data, (mapped to mm9). The following example shows that we first specify paths toĮxample BAM files in the TBX20BamSubset (Bindreither 2018) data package. The package reads BAM file(s) to obtain read coverage information in different 10.6 Significantly regulated APA in Intron.10.5 Significantly regulated APA in 3’UTRs.10.4 Calculation of relative expression of 3’UTR APA and IPA.10 Complete Analysis Example: APA analysis in mouse testis versus heart.9 Extract 3’most alignment from the pair-end bam file.8 Gene expression analysis using coding regions.6.2 Significantly regulated APA in introns.6.1 Significantly regulated APA in 3’UTRs.3.4 Building 3’UTR PAS and IPA reference using GTF files.3.3 Building 3’UTR and intronic PAS reference region at once.
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