A collection of scripts for use on Sanger HPC to manage downloading, relaligning, and pre-processing
A script to download from IRODS data using LSF scheduling.
Following download it will extract reads from downloaded cram files using samtools fastq then align those
fastq to hg19 reference genome using either BWA mem or star depending on if provided with argument 'RNA' or 'DNA'.
e.g. to download and process RNA data from lane 1 of run 12345
irods_download_remap_pipeline.sh 12345 1 RNA