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Star aligner manual. STAR 2.5.3a aligner |
Star aligner manual.STAR aligner
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Latest commit. Git stats 1, commits. Failed to load latest commit information. View code. STAR 2. MIT license. Code of conduct. A gap in the alignment between a read and the genome that is smaller is considered a deletion, not an intron. Maximum size of intron. If a read aligns to the genome with a gap larger than this it is considered a chimeric read.
The default value of , is fine-tuned to mammalian genomes, for plant and yeast genomes you will have to decrease it. Maximum distance between mate pair reads. If reads map to the genome farther apart the fragment is considered to be chimeric. Maximum alignments per read -parameter sets the maximum number of loci the read is allowed to map to.
Alignments all of them will be output only if the read maps to no more loci than this value. Figure 2: Configuration Page. Output Save Splice Junctions: Save high confidence collapsed splice junctions in tab-delimited format.
Figure 3: Output Page. Each alignment line has 11 mandatory fields for essential alignment information such as the mapping position, and a variable number of optional fields for flexible or aligner specific information: SAM Format Description.
Read is mapped in a proper pair. Read is unmapped. Mate is unmapped. Read reverse strand. Mate reverse strand. Read is from the first pair. Read is from the second pair. Alignment isn't primary. Read is PCR or optical duplicate. Operators are: M: Align match. I: Insertion to the reference. D: Deletion from the reference. N: Skipped region from the reference.
S: Soft clipping. H: Hard clipping. P: Padding silent deletion from padded reference. TLEN : Signed observed template length. SEQ : Segment sequence. The columns have the following meaning: Chromosome.
The first base of the intron 1-based. The last base of the intron 1-based. Strand: 0: undefined.
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