Read mapping with BWA-MEM

The NGS reads of this project are aligned against the reference genome sequence using the highly variant tolerant short read aligner BWA-MEM (Li , 2013; Li et al., 2009). The parameter settings of the aligner are defined in the bwa.param file.

args <- systemArgs(sysma="param/bwa.param", mytargets="targets.txt")
sysargs(args)[1] # Command-line parameters for first FASTQ file

Runs the alignments sequentially (e.g. on a single machine)

system("bwa index -a bwtsw ./data/tair10.fasta")
bampaths <- runCommandline(args=args)
writeTargetsout(x=args, file="targets_bam.txt", overwrite=TRUE)

Alternatively, the alignment jobs can be submitted to a compute cluster, here using 72 CPU cores (18 qsub processes each with 4 CPU cores).

system("bwa index -a bwtsw ./data/tair10.fasta")
resources <- list(walltime="1:00:00", ntasks=1, ncpus=cores(args), memory="10G")
reg <- clusterRun(args, conffile=".BatchJobs.R", template="slurm.tmpl", Njobs=18, runid="01",
writeTargetsout(x=args, file="targets_bam.txt", overwrite=TRUE)

Check whether all BAM files have been created


Read and alignment stats

The following generates a summary table of the number of reads in each sample and how many of them aligned to the reference.

read_statsDF <- alignStats(args=args) 
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

The symLink2bam function creates symbolic links to view the BAM alignment files in a genome browser such as IGV. The corresponding URLs are written to a file with a path specified under urlfile, here IGVurl.txt.

symLink2bam(sysargs=args, htmldir=c("~/.html/", "projects/gen242/"), 

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