STAR on Helix
STAR aligns RNA-seq reads to a reference genome.
Its advantages include:
- 'Ab initio' splice junctions --un-annotated, non-canonical, distal exons, chimeric ...
- Unique and multiple mappers
- Any read length, any number of splice junctions per read
- Any (reasonable) number of mismatches and indels
- Alignment scoring utilizing Illumina quality scores
- "Auto" trimming of poor quality ends
- poly-A tails detection
- Very Fast: human 75-mer reads: 60 Million read per hour
The STAR executable can be added to your path by typing 'module load STAR'.
How To Use
helix% module load STAR helix% STAR --runMode genomeGenerate --genomeDir /fdb/genome/ \ --genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 --runThreadN 4 ... helix %
Note that you should run a maximum of 4 threads on Helix.
