Pipelinescript

[ewallace]

prepRiboviz.sh

Shell script for preparing ribosome profiling data for RiboViz or other analysis, that

- processes all fastq.gz files in an input directory (-in),

- cuts out sequencing library adapters (CTGTAGGCACC or -adapters)

- removes rRNA or other contaminating reads by hisat2 alignment to rRNA index file (-rRNA)

- aligns remaining reads to ORFs or other hisat2 index file (-orf)

- trims 5' mismatches from reads and removes reads with more than 2 mismatches

- parallelizes over many processes (-p), except for cutadapt which isn't parallel

- puts all intermediate files into a temporary directory (-tmp)

- when finished, the script will put useful output files in another directory (-out)

Note that the bamfiles ${fn_outbam} are directly usable in genome browsers, etc.

Currently this makes the bamfiles and leaves temp files in place.

Next step is to pass bam output into hdf5 and visualization tools.