Alignment statistics

Description

Generate data frame containing important read alignment statistics such as the total number of reads in the FASTQ files, the number of total alignments, as well as the number of primary alignments in the corresponding BAM files.

Usage

alignStats(args)

Arguments

Value

data.frame with alignment statistics.

Author(s)

Thomas Girke

Examples

## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
args
names(args); modules(args); cores(args); outpaths(args); sysargs(args)

## Not run: 
## Execute SYSargs on single machine
runCommandline(args=args)

## Execute SYSargs on multiple machines  
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00")
qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR")
## Alignment stats
read_statsDF <- alignStats(args) 
read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

## End(Not run)