Why is it called a sashimi plot?
Why is it called a sashimi plot?
Why is it called sashimi_plot? ¶ We chose “Sashimi” because our tool plots the raw RNA-Seq data in addition to inferences made about the RNA-Seq reads (hat tip to Vincent Butty.) Also, the variations and various “bumps” in exonic read densities in RNA-Seq data look a bit like rolls of Sashimi.
How do you use IGV?
Using IGV: Examples
- Open IGV (.igv.sh from command line)
- Load the human genome : In the toolbar, Click Genome > Load Genome from Server > Search and select Human (hg19)
- Load the encode RNA-Seq BAM files: Go to File > Load from ENCODE > Select C2C12 RNA-Seq BAM files (See image in the Pdf)
How do you scale in IGV?
IGV determines the default data range for a track as described in Default Display. To change the data range for selected heat map tracks: Right-click a track and select Set Heatmap Scale from the pop-up menu. The heatmap scale can be set per track.
What does IGV stand for?
The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources.
How do you read IGV?
Hover over or click a read to view information about the read, including the location of its paired mate. IGV colors (1) paired end reads with inferred insert size smaller or larger than expected; (2) read with mate that is aligned to a different chromosome; (3) paired-end alignments with deviant pair orientation.
What are splicing signals?
Splice-junction sequence signals are strongly conserved structural components of eukaryotic genes. These sequences border exon/intron junctions and aid in the process of removing introns by the RNA splicing machinery.
How do I read IGV data?