7.1 .fasta vs .fastq

.fasta file starts with >

Fastq file has four components Fastq scores depend on the sequencing platform ## Quality check with Rqc

Rqc tutorial

library(Rqc)
folder = system.file(package="ShortRead", "extdata/E-MTAB-1147")

# feeds fastq.qz files to quality check function
qcRes=rqc(path = folder, pattern = ".fastq.gz")

# try with long read data... not nearly as useful
qcResC=rqc(path = "example_files/example_fastqgz", pattern = ".fastq.gz")

long read analysis

An alternative: fastqcr (CRNA not Bioconductor) for lots of fastq files! UNIX/MAC ONLY

fastqcr tutorial

library(fastqcr)
fastqc_install()
fastqc(fq.dir = folder,qc.dir = "fastqc_results")

# view the report rendered by R functions
qc_report(qc.path="fastqc_results", 
          result.file="reportFile", preview = TRUE)