The NGS reads of this project will be aligned against the reference genome
sequence using Bowtie2/TopHat2 (Kim et al., 2013; Langmead et al., 2012). The
parameter settings of the aligner are defined in the tophat.param
Submission of alignment jobs to compute cluster, here using 72 CPU cores (18 qsub processes each with 4 CPU cores).
Alignment with Rsubread
The following example shows how one can use within the systemPipeR environment the R-based
aligner Rsubread or other R-based functions that read from input files and write to output files.
Read mapping with HISAT2
Check whether all BAM files have been created
Read and alignment stats
The following provides an overview of the number of reads in each sample
and how many of them aligned to the reference.
Create symbolic links for viewing BAM files in IGV
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 in the results directory.