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12회 업데이트 됨.

  • 최초 작성자
  • 최근 업데이트

Structured data


STAR (Spliced Transcripts Alignment to a Reference) #

STAR란? 참조 #

  • Ultrafast universal RNA-seq aligner이다.
  • 기존 aligner의 error rates, speed, length limitation 및 biaes등의 한계를 개선하였다.
  • 공인되어 많이 사용되어 지고 있는 타 RNAseq aligner에 비해 수십/수백배까지 빠른 속도로 mappging이 수행됨과 동시에 정확성, biases, canonical junction, chimeric, full-length RNA sequence에 대해 개선된 결과를 제공한다.

Tophat과 비교 #


기본사용법 (tuxedo protocol 에서 tophat 파트 대용) #

  • 인덱싱: STAR --runMode genomeGenerate --runThreadN 24 --genomeDir ./ --genomeFastaFiles genome.fa
  • 매핑: STAR --genomeDir /mnt/tw/ref/mm10_STARidx/ --genomeLoad NoSharedMemory --runThreadN 48 --readFilesIn ${sp}.R1.fq ${sp}.R2.fq --outFileNamePrefix ${sp}.STAR
  • (input이 gzipped files (*.gz) 압축인 경우, --readFilesCommand zcat 또는 --readFilesCommand gzip -c 옵션사용)

The basic options to run a mapping job are as follows: #

  • --runThreadN NumberOfThreads
  • --genomeDir /path/to/genomeDir
  • --readFilesIn /path/to/read1 [/path/to/read2 ]
  • --runThreadN option defines the number of threads to be used for genome generation, it has to be set to the number of available cores on the server node.
  • --genomeDir specifies path to the genome directory where genome indices where generated
  • --readFilesIn name(s) (with path) of the files containing the sequences to be mapped (e.g.RNA-seq FASTQ files). If using Illumina paired-end reads, the read1 and read2 files have to be supplied. STAR can process both FASTA and FASTQ files. Multi-line (i.e. sequence split in multiple lines) FASTA file are supported. If the read files are compressed, use the
  • --readFilesCommand UncompressionCommand option, where UncompressionCommand is the un-compression command that takes the file name as input parameter, and sends the uncompressed output to stdout. For example, for gzipped files (*.gz) use --readFilesCommand zcat OR --readFilesCommand gzip -c. For bzip2-compressed files, use --readFilesCommand bzip2 -c.

Incoming Links #

Related Bioinformaticses #

Suggested Pages #