## ----eval=TRUE----------------------------------------------------------- library(scPipe) library(SingleCellExperiment) data_dir = tempdir() ## ------------------------------------------------------------------------ # file path: ERCCfa_fn = system.file("extdata", "ERCC92.fa", package = "scPipe") ERCCanno_fn = system.file("extdata", "ERCC92_anno.gff3", package = "scPipe") barcode_annotation_fn = system.file("extdata", "barcode_anno.csv", package = "scPipe") ## ----eval=TRUE----------------------------------------------------------- fq_R1 = system.file("extdata", "simu_R1.fastq.gz", package = "scPipe") fq_R2 = system.file("extdata", "simu_R2.fastq.gz", package = "scPipe") ## ----eval=TRUE----------------------------------------------------------- sc_trim_barcode(file.path(data_dir, "combined.fastq"), fq_R1, fq_R2, read_structure = list(bs1=-1, bl1=0, bs2=6, bl2=8, us=0, ul=6)) ## ----eval=TRUE----------------------------------------------------------- if(.Platform$OS.type != "windows"){ Rsubread::buildindex(basename=file.path(data_dir, "ERCC_index"), reference=ERCCfa_fn) Rsubread::align(index=file.path(data_dir, "ERCC_index"), readfile1=file.path(data_dir, "combined.fastq"), output_file=file.path(data_dir, "out.aln.bam"), phredOffset=64) } ## ----eval=TRUE----------------------------------------------------------- if(.Platform$OS.type != "windows"){ sc_exon_mapping(file.path(data_dir, "out.aln.bam"), file.path(data_dir, "out.map.bam"), ERCCanno_fn) } ## ----eval=TRUE----------------------------------------------------------- if(.Platform$OS.type != "windows"){ sc_demultiplex(file.path(data_dir, "out.map.bam"), data_dir, barcode_annotation_fn,has_UMI=FALSE) sc_gene_counting(data_dir, barcode_annotation_fn) } ## ------------------------------------------------------------------------ if(.Platform$OS.type != "windows"){ sce = create_sce_by_dir(data_dir) dim(sce) } ## ------------------------------------------------------------------------ data("sc_sample_data") data("sc_sample_qc") sce = SingleCellExperiment(assays = list(counts = as.matrix(sc_sample_data))) # generate new sce with gene count matrix QC_metrics(sce) = sc_sample_qc demultiplex_info(sce) = cell_barcode_matching UMI_dup_info(sce) = UMI_duplication ## ------------------------------------------------------------------------ plot_demultiplex(sce) ## ------------------------------------------------------------------------ plot_UMI_dup(sce) ## ---- warning=FALSE, message=FALSE--------------------------------------- sce = calculate_QC_metrics(sce) sce = detect_outlier(sce) ## ------------------------------------------------------------------------ plot_mapping(sce, percentage = TRUE, dataname = "sc_sample_data") ## ------------------------------------------------------------------------ plot_QC_pairs(sce) ## ------------------------------------------------------------------------ sce = remove_outliers(sce) dim(sce) ## ------------------------------------------------------------------------ sessionInfo()