What is the drawback of star alignment?
Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
Does Star Align to genome or transcriptome?
STAR—Alignment with STAR to the target genome (aided with the GTF annotation of the transcriptome) and projected to the transcriptome allowing alignments with indels and soft clipping, followed by quantification using Salmon in alignment mode.
What is Star sequencing?
In astronomy, the main sequence is a continuous and distinctive band of stars that appears on plots of stellar color versus brightness. These color-magnitude plots are known as Hertzsprung–Russell diagrams after their co-developers, Ejnar Hertzsprung and Henry Norris Russell.
What is Star aligner?
Spliced Transcripts Alignment to a Reference (STAR) is a fast RNA-seq read mapper, with support for splice-junction and fusion read detection. STAR aligns reads by finding the Maximal Mappable Prefix (MMP) hits between reads (or read pairs) and the genome, using a Suffix Array index.
What is a splice aware aligner?
A splice-aware aligner would know not to try to align RNA-seq reads to introns, and would somehow identify possible downstream exons and try to align to those instead, ignoring introns altogether.
How much memory does star aligner use?
12 threads . 6 threads . 12 threads . STAR’s high mapping speed is traded off against RAM usage: STAR requires ∼27 GB of RAM for aligning to the human genome.
What is a good alignment rate?
Our typical value is 15-20. % of reads mapped to too many loci | 0.09% : by default “too many loci” is >10, but this number is good so you are not missing much.
What is in SAM file?
The Sequence Alignment/Map (SAM) is a file format to save alignment information of short reads mapped against reference sequences. It usually starts with a header section followed by alignment information as tab separated lines for each read. Header section. @HD VN:1.3 SO:coordinate. @SQ SN:conticA LN:443.
What is a BigWig file?
BigWig files are created from wiggle (wig) type files using the program wigToBigWig . The bigWig files are in an indexed binary format. The main advantage of this format is that only those portions of the file needed to display a particular region are transferred to the Genome Browser server.