IGV: how to view large (>1MB) fragment in a window

[shuang]

I want to view the distribution of number of short reads aligned to a genome. How to view large (>1MB) fragment, even 1 chromosome, in a window.

Currently, I only can scroll the window manually and view 40kb at a time? When I zoom out more, the alignment window would become blank.

[Jim Robinson]

Hi, you can increase the window size for the track in view by right-clicking, or globally from the user preferences window. However, there is a limit as your machine does not have an unlimited amount of memory. 1 MB might be o.k. for rna-seq data, as it is sparse, experiment with different sizes and try.

For whole chromosome you can view coverage by computing a "TDF" file with igvtools, or alternatively load a bigwig computed by some other means. Even if you could load all your rna alignments at whole chromosome level the only meaningful information you could see is coverage.

The igv user guide has a section specifically on alignment viewing options, a direct link is here.

http://www.broadinstitute.org/software/igv/AlignmentData

-- Jim