# STAR 2.7.9a


## STAR 2.7.9a - Spliced Transcripts Alignment to a Reference

### Abstract

**Motivation:** Accurate alignment of high-throughput RNA-seq data is a challenging
and yet unsolved problem because of the non-contiguous transcript structure,
relatively short read lengths and constantly increasing throughput of the
sequencing technologies. Currently available RNA-seq aligners suffer from high
mapping error rates, low mapping speed, read length limitation and mapping
biases.

**Results:** To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq
dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR)
software based on a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays followed
by seed clustering and stitching procedure. STAR outperforms other aligners by
a factor of >50 in mapping speed, aligning to the human genome 550 million
2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the
same time improving alignment sensitivity and precision. In addition to unbiased
de novo detection of canonical junctions, STAR can discover non-canonical
splices and chimeric (fusion) transcripts, and is also capable of mapping
full-length RNA sequences. Using Roche 454 sequencing of reverse transcription
polymerase chain reaction amplicons, we experimentally validated 1960 novel
intergenic splice junctions with an 80-90% success rate, corroborating the high
precision of the STAR mapping strategy.

Location and version:

```console
$ which STAR
/local/cluster/bin/STAR
$ STAR --version
2.7.9a
```

help message (abbreviated):

```console
$ STAR --help
Usage: STAR  [options]... --genomeDir /path/to/genome/index/   --readFilesIn R1.fq R2.fq
Spliced Transcripts Alignment to a Reference (c) Alexander Dobin, 2009-2020

STAR version=2.7.9a
STAR compilation time,server,dir=2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
For more details see:
<https://github.com/alexdobin/STAR>
<https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf>
### versions
versionGenome           2.7.4a
    string: earliest genome index version compatible with this STAR release. Please do not change this value!

### Parameter Files
parametersFiles          -
    string: name of a user-defined parameters file, "-": none. Can only be defined on the command line.

### System
sysShell            -
    string: path to the shell binary, preferably bash, e.g. /bin/bash.
                    - ... the default shell is executed, typically /bin/sh. This was reported to fail on some Ubuntu systems - then you need to specify path to bash.

### Run Parameters
runMode                         alignReads
    string: type of the run.

                                alignReads             ... map reads
                                genomeGenerate         ... generate genome files
                                inputAlignmentsFromBAM ... input alignments from BAM. Presently only works with --outWigType and --bamRemoveDuplicates.
                                liftOver               ... lift-over of GTF files (--sjdbGTFfile) between genome assemblies using chain file(s) from --genomeChainFiles.
                                soloCellFiltering  </path/to/raw/count/dir/>   </path/to/output/prefix>    ... STARsolo cell filtering ("calling") without remapping, followed by the path to raw count directory and output (filtered) prefix
```

STAR is useful for spliced alignments of RNA-Seq reads to an assembled genome.

software ref: <https://github.com/alexdobin/STAR>  
research ref: <https://doi.org/10.1093/bioinformatics/bts635>