IGV - Integrative Genomics Viewer

Load packages and data

We’re going to use the RNA sequencing experiment in the passilaBamSubset package.

#biocLite("pasillaBamSubset")
#biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
library(pasillaBamSubset)
#Genes annotated in transcript database
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
#The 2 files of interest
fl1 <- untreated1_chr4()
fl2 <- untreated3_chr4()

IGV - Integrative Genomics Viewer

IGV is freely available for download here.

Copy fl1 and fl2 from the R library directory to the current working directory.

We need to use the `Rsamtools` library to index the BAM files for using IGV.

file.copy(from=fl1,to=basename(fl1))

## [1] FALSE

file.copy(from=fl2,to=basename(fl2))

## [1] FALSE

library(Rsamtools)
indexBam(basename(fl1))

##       untreated1_chr4.bam 
## "untreated1_chr4.bam.bai"

indexBam(basename(fl2))

##       untreated3_chr4.bam 
## "untreated3_chr4.bam.bai"

Note that if you have trouble downloading IGV, another option for visualization is the UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgTracks 
  
The UCSC Genome Browser is a great resource, having many tracks involving gene annotations, conservation over multiple species, and the ENCODE epigentic tracks is already available. However, the UCSC Genome Browser requires that you upload your genomic files to their server, or put your data on a publicly available server. This is not always possible if you are working with confidential data.

Using IGV, look the gene lgs.

In this example the data is an RNA sequencing experiment of Drosophila. From IGV, we need to use the Drosophila melanogaster genome, and specifically the dm3 genome.

Load the 2 bam files: File -> load from file -> select the 2 bam files. Two new tracks are created (one track for each file).

The passilaBamSubset package is a subset of the reads, which map to chromosome 4. Select chromosome 4, type the gene name lgs in the search field, and click Go. We can see that the coverage only is on the exons, mostly.

And if we zoom in (hold Shift, and drag on the top part to zoom) you can see the individual reads. There are reads on the plus strand and minus strand. IGV is a very useful program for visualizing quickly reads from sequencing experiments.

Legend: 1 = Reads on the plus strand 2 = Reads on the minus strand 3 = Mismatch base compared to the reference genome

Video : Visualizing NGS data with IGV

(French)

In the next unit, I'm going to show how to generate coverage plots-- like the ones in here-- but within Bioconductor.

Footnotes

• IGV https://www.broadinstitute.org/igv/home

• UCSC Genome Browser: zooms and scrolls over chromosomes, showing the work of annotators worldwide http://genome.ucsc.edu/

Licence

Licence

References

https://github.com/genomicsclass

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