## ----setup, echo=FALSE, results="hide", include = FALSE------------------------------------------- knitr::opts_chunk$set(tidy=FALSE, cache=FALSE, #dev="png", message=FALSE, error=FALSE, warning=TRUE) options(width=100) ## ----getPackage, eval=FALSE----------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Rfastp") ## ----eval = FALSE--------------------------------------------------------------------------------- # BiocManager::install("remotes") # BiocManager::install("RockefellerUniversity/Rfastp") ## ------------------------------------------------------------------------------------------------- library(Rfastp) ## ------------------------------------------------------------------------------------------------- se_read1 <- system.file("extdata","Fox3_Std_small.fq.gz",package="Rfastp") pe_read1 <- system.file("extdata","reads1.fastq.gz",package="Rfastp") pe_read2 <- system.file("extdata","reads2.fastq.gz",package="Rfastp") outputPrefix <- tempfile(tmpdir = tempdir()) ## ------------------------------------------------------------------------------------------------- se_json_report <- rfastp(read1 = se_read1, outputFastq = paste0(outputPrefix, "_se"), thread = 4) ## ------------------------------------------------------------------------------------------------- pe_json_report <- rfastp(read1 = pe_read1, read2 = pe_read2, outputFastq = paste0(outputPrefix, "_pe")) ## ------------------------------------------------------------------------------------------------- pe_merge_json_report <- rfastp(read1 = pe_read1, read2 = pe_read2, merge = TRUE, outputFastq = paste0(outputPrefix, '_unpaired'), mergeOut = paste0(outputPrefix, "_merged.fastq.gz")) ## ------------------------------------------------------------------------------------------------- umi_json_report <- rfastp(read1 = pe_read1, read2 = pe_read2, outputFastq = paste0(outputPrefix, '_umi1'), umi = TRUE, umiLoc = "read1", umiLength = 16) ## ----umi------------------------------------------------------------------------------------------ umi_json_report <- rfastp(read1 = pe_read1, read2 = pe_read2, outputFastq = paste0(outputPrefix, '_umi2'), umi = TRUE, umiLoc = "read1", umiLength = 16, umiPrefix = "#", umiNoConnection = TRUE, umiIgnoreSeqNameSpace = TRUE) ## ------------------------------------------------------------------------------------------------- clipr_json_report <- rfastp(read1 = se_read1, outputFastq = paste0(outputPrefix, '_clipr'), disableTrimPolyG = TRUE, cutLowQualFront = TRUE, cutFrontWindowSize = 29, cutFrontMeanQual = 20, cutLowQualTail = TRUE, cutTailWindowSize = 1, cutTailMeanQual = 5, minReadLength = 29, adapterSequenceRead1 = 'GTGTCAGTCACTTCCAGCGG' ) ## ------------------------------------------------------------------------------------------------- pe001_read1 <- system.file("extdata","splited_001_R1.fastq.gz", package="Rfastp") pe002_read1 <- system.file("extdata","splited_002_R1.fastq.gz", package="Rfastp") pe003_read1 <- system.file("extdata","splited_003_R1.fastq.gz", package="Rfastp") pe004_read1 <- system.file("extdata","splited_004_R1.fastq.gz", package="Rfastp") inputfiles <- c(pe001_read1, pe002_read1, pe003_read1, pe004_read1) cat_rjson_report <- rfastp(read1 = inputfiles, outputFastq = paste0(outputPrefix, "_merged1")) ## ------------------------------------------------------------------------------------------------- pe001_read2 <- system.file("extdata","splited_001_R2.fastq.gz", package="Rfastp") pe002_read2 <- system.file("extdata","splited_002_R2.fastq.gz", package="Rfastp") pe003_read2 <- system.file("extdata","splited_003_R2.fastq.gz", package="Rfastp") pe004_read2 <- system.file("extdata","splited_004_R2.fastq.gz", package="Rfastp") inputR2files <- c(pe001_read2, pe002_read2, pe003_read2, pe004_read2) catfastq(output = paste0(outputPrefix,"_merged2_R2.fastq.gz"), inputFiles = inputR2files) ## ------------------------------------------------------------------------------------------------- dfsummary <- qcSummary(pe_json_report) ## ------------------------------------------------------------------------------------------------- p1 <- curvePlot(se_json_report) p1 ## ------------------------------------------------------------------------------------------------- p2 <- curvePlot(se_json_report, curve="content_curves") p2 ## ------------------------------------------------------------------------------------------------- dfTrim <- trimSummary(pe_json_report) ## ------------------------------------------------------------------------------------------------- ?rfastp ## ------------------------------------------------------------------------------------------------- ?catfastq ## ------------------------------------------------------------------------------------------------- ?qcSummary ## ------------------------------------------------------------------------------------------------- ?trimSummary ## ------------------------------------------------------------------------------------------------- ?curvePlot ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()