Advanced Options

Enter a number 1–5. The default is 1.

When a read aligns to multiple loci, the alignment is reported if its score is in the range of (s - value, s], where "s" is the highest alignment score and "value" is the number that you entered.

Enter a number 1–21. The default is 10.

The output includes alignments that have fewer mismatches than this value.

Enter a number 0–0.5. The default is 0.3.

The output includes alignments that have a ratio of mismatches to mapped length that is less than this value.

Enter a number 0.33–1. The default is 0.66.

The output includes alignments that have a score higher than this value. The score is normalized by read length, which is the length sum of mates for paired-end reads.

Enter a number 0.33–1. The default is 0.66.

The output includes alignments that have matched bases higher than this value. The number is normalized by reads length, which is the length sum of mates for paired-end reads.

Enter a number 30–1,000. The default is 50.

The seed search starts at position 1 and the step length determines the next start position. The step length cannot be longer than this value.

Enter a number 10–Maximum Intron Size. The default is 21.

The genomic gap is considered intron when its length is greater or equal to this value. Otherwise, the gap is considered a deletion.

Enter 0 or a number Minimum Intron Size–1,000,000. The default is 0.

If the value is set to 0, STAR calculates the maximum intron size.