STAR

Build a database

$ /path/to/star/STAR --runMode genomeGenerate --genomeDir <dir_name> \
 --genomeFastaFiles <fasta_file> --runThreadN <number of threads>

For transcript database, use '--genomeChrBinNbits 10 --genomeSAindexNbases 10' additionally (see section 2.2 in the manual).

Map single-end reads

 $STAR --genomeDir $DB --readFilesIn $FQ--runThreadN 12
 mv Aligned.out.sam $SAM

Map paired-end reads

 $STAR --genomeDir $DB --readFilesIn $FQ1 $FQ2 --runThreadN 12
 mv Aligned.out.sam $SAM

See also

• Project home - https://github.com/alexdobin/STAR
• Paper - http://bioinformatics.oxfordjournals.org/content/29/1/15
• Manual - https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

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