Difference between revisions of "STAR"
From XenopusBioinfo
TaejoonKwon (Talk | contribs) (→Build a database) |
TaejoonKwon (Talk | contribs) |
||
| Line 4: | Line 4: | ||
For transcript database, use '--genomeChrBinNbits 10 --genomeSAindexNbases 10' additionally (see section 2.2 in the manual). | 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 == | == See also == | ||
Latest revision as of 14:39, 17 November 2014
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
