Advanced Options

Enter a number between 0 and 5. The default is 2.

Alignments with more than the number of mismatches are discarded.

Enter a number between 0 and 5. The default is 2.

Alignments with more than the total length of gaps are discarded.

Enter a number between 0 and 10. The default is 2.

Alignments with more than the selected edit distance are discarded.

Enter a number between 0 and 300. The default is 50.

The expected (mean) inner distance between mate pairs. For paired-end runs with fragments selected at 300 bp, where each end is 50 bp, set this value at 200.

Enter a number between 1 and 100. The default is 20.

The standard deviation of the distribution on inner distances between mate pairs.

Enter a number between 10 and the maximum intron length. The default is 70.

TopHat ignores donor/acceptor pairs closer than the specified number of bases.

Enter a number between the minimum intron length and 1,000,000. The default is 500,000.

When searching for junctions, TopHat ignores donor/acceptor pairs farther than the specified number of bases, except when a pair is supported by a split segment alignment of a long read.

Enter a number between 0 and 5. The default is 3.

Enter a number between 1 and 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 between 1 and 21. The default is 10.

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

Enter a number between 0 and 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 between 0.33 and 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 between 0.33 and 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 between 30 and 1000. 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 between 10 and the 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 between the minimum intron size and 1,000,000. The default is 0.

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

Select the checkbox to use splice junction information in the annotation. By default, the checkbox is selected.

Compatible—Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator.

Total—Cufflinks counts all fragments, including the fragments not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. This option is the default.

Enter a number between 0.05 and 1. The default is 0.1.

After calculating isoform abundance for a gene, Cufflinks filters out transcripts that are low abundance. Isoforms that are expressed at low levels often cannot be reliably assembled.

The isoforms can be artifacts of incompletely spliced precursors of processed transcripts. This parameter filters out introns that have fewer supporting sliced alignments.

Enter a number between 0 and 1. The default is 0.15.

Some RNA-seq protocols produce a significant number of reads that come from incompletely spliced transcripts. These reads can confound the assembly of fully spliced mRNAs.

Cufflinks uses this parameter to filter out alignments that are within the intronic intervals. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads. If the result is lower than the value in this parameter, the intronic alignments are ignored.

Enter a number between 10 and the maximum intron length. The default is 50.

Enter a number between the minimum intron length and 600,000. The default is 300,000.

When the intron length is longer than this value, Cufflinks does not report transcripts with introns and excludes SAM alignments with REF_SKIP CIGAR operations.

Cuffquant/Cufflinks runs bias detection and correction algorithm, which can improve accuracy of transcript abundance estimates.

Cuffquant/Cufflinks runs an initial estimation procedure to weight reads mapping to multiple locations in the genome more accurately.