How do I check my IGV coverage?
How do I check my IGV coverage?
By default IGV dynamically calculates and displays the default coverage track for an alignment file. When IGV is zoomed to the alignment read visibility threshold (by default, 30 KB), the coverage track displays the depth of the reads displayed at each locus as a gray bar chart.
What is an IGV file?
An IGV file (. igv) is a tab-delimited text file that defines tracks. The first row contains column headings for chromosome, start location, end location, and feature followed by the name of each track defined in the . igv file. Each subsequent row contains a locus and the associated numeric values for each track.
How do I open IGV files?
Select File>Load from File. IGV displays the Select Files window. Select one or more data files or sample information files, then click OK.
What is BAM index file?
A bam file is a binary blob that stores all of your aligned sequence data. You can view what’s in the bam file using “samtools view bamfile. bam | less”. Bam files can also have a companion file, called an index file. This file has the same name, suffixed with .
How do I view BAM files in IGV?
In IGV, select File > Load from URL … A window will pop up and ask you to give the correct URL for the file you want to view. Paste in the URL and the file will be downloaded. From the file extension, IGV will automatically treat the information in the file accordingly.
How do I run IGV on Linux?
Download and unzip the binary distribution archive in a folder of your choosing. IGV is launched from a command prompt — follow the instructions in the readme file. To launch IGV on Mac or Linux use the shell script igv.sh.
How do I install genome in IGV?
Select the genome you would like to add to the IGV genomes menu, and click ‘OK’. A new entry will be inserted in the drop-down list (in alphabetical order), and the display will switch to this genome. Checking the ‘Download sequence’ box will also download a FASTA file of the whole genome sequence for offline use.
What are BAM files used for?
bam) is the compressed binary version of a SAM file that is used to represent aligned sequences up to 128 Mb. SAM and BAM formats are described in detail at https://samtools.github.io/hts-specs/SAMv1.pdf. BAM files use the file naming format of SampleName_S#.
What is in a SAM file?
SAM files are a type of text file format that contains the alignment information of various sequences that are mapped against reference sequences. These files can also contain unmapped sequences. Since SAM files are a text file format, they are more readable by humans and will be used as the examples for this section.