Expanded visualization for BED file with non-overlapping regions

[Onconetwork Univr]

Hi,

After the update to IGV 2.17 I found I was missing a "feature" that came quite handy.

I have a BED file with non overlapping regions (i.e. each region is separated from the other by 1 base, so they are juxtaposed but not overlapping).

Version 2.16 visualized that file in 2 rows when in the "expanded" mode.

Version 2.17 splits the visualization in 2 rows only if there is at least one base overlap.

Is it possible to tweak the settings so that IGV splits my BED file into 2 rows as it did in 2.16 version?

Thank you for your help

Cheers

Andrea

[igv-help]

I will look into this, I'm not sure that change was intentional.   There are no settings for this.

[Onconetwork Univr]

Hi,

did you have any luck with the "issue" I posted about? The behavior in 2.18.1 is the same of 2.17.x

Thank you,

Andrea

[James Robinson]

Hi,

I looked into this.   In IGV 2.16 and earlier there was no gap between adjacent features, so the features weren't distinguishable unless on separate rows.  IGV version 2.17 and later add a gap between adjacent features, and place them on the same row.    This is as designed, and there are no settings for this.   If you want features on separate rows you can either split them into 2 bed files, or add an artificial 1 base overlap.

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[Andrea Mafficini]

Thank you James!

Kind regards, 

Andrea