STAR
From XenopusBioinfo
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