display deleted sequences in Alignments2 tracks

[keiranmraine]

Could the ability to optionally show the reference sequence of deleted regions of reads rather than * be added?

Thanks

[cmdcolin]

This seems slightly confusing. I can see the benefit of being able to quickly see the "replaced" base, but only doing it for the deleted feature seems strange. I am imagining an alternative that is like a button that let's you toggle all snps to show the original base.

-Colin

[keiranmraine]

I've only requested for deletions as it isn't possible (currently) to zoom in enough for the sequence to be displayed on the reads (unless I've missed something). In GBrowse you could display 2 bases across the whole width of the display and inserted seq would be visible.

By optional I actually mean via track config rather than by clicking a check-box.

[cmdcolin]

Here on the sample browser, there is a deletion (indicated by the '*'). And if i am folllowing, this would have a configuration to display the reference base?

http://jbrowse.org/code/JBrowse-1.11.3/?loc=ctgA%3A3839..3890&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2Cvolvox-sorted-vcf%2Cvolvox-sorted_bam_coverage%2Cvolvox-sorted_bam&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&nav=1&overview=1

[keiranmraine]

Yes, still with the grey background and white text though (otherwise it would look like a run of subs). Obviously if the read didn't have an MD tag it should default to *.

In the case of events where, 6 bases are deleted and 4 bases are inserted it all gets messy (delete 6T, insert 4G). For these you want the inserted seq to look like a run of subs but the base spacing would have to be averaged across the available space.

[iCOMDEX]

среда, 30 апреля 2014 г. пользователь Keiran Raine написал:

Yes, still with the grey background and white text though (otherwise it would look like a run of subs). Obviously if the read didn't have an MD tag it should default to *.

In the case of events where, 6 bases are deleted and 4 bases are inserted it all gets messy (delete 6T, insert 4G). For these you want the inserted seq to look like a run of subs but the base spacing would have to be averaged across the available space.

— Reply to this email directly or view it on GitHubhttps://github.com/GMOD/jbrowse/issues/464#issuecomment-41806099 .Г

[cmdcolin]

I was thinking perhaps a mouseover popup to show the deleted/inserted sequence would be nice. Would this work?

[keiranmraine]

That would be very useful.

[cmdcolin]

the work on https://github.com/GMOD/jbrowse/pull/795 revealed that the sequence of the deletion is actually embedded in the MD tag which makes it easier in most cases to get that data

[rbuels]

Sounds like the consensus is that mousing over the '*' deletion marker would show a tooltip with the deleted sequence? That wouldn't allow users to cut and paste the deleted sequence. Would that be something people would want to do?

[cmdcolin]

Note that this could apply to SNPCoverage too, and could show insertions

[jmercier-lbi]

Thanks @cmdcolin , Following issue #1425 it would ease the analysis interpretation of alignment if the SNPCoverage display the sequence inserted and deleted And about Alignment2 track Is it possible to add a javascript event when the mouse is over an insertion/deletion and to display also the sequence inserted/deleted?

thanks