Details
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Type:
Support
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Labels:None
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Epic Link:
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Sprint:Sprint 18
Description
Short list:
-UCSC Genome Browser
-Jalview
-Artemis
-IGV
-Gbrowse/Jbrowse
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
This story was created to serve as a reminder for the task of examining other genome browsers to gain improvement ideas that can be applied to IGB.
*Genome browser to examine include: -UCSC Genome Browser -Jalview -Artemis, Ensemble, |
This story was created to serve as a reminder for the task of examining other genome browsers to gain improvement ideas that can be applied to IGB.
*Genome browser to examine include: -UCSC Genome Browser (most popular) -Jalview -Artemis -Ensemble -IGV -Gbrowse/Jbrowse |
| Issue Type | Bug [ 1 ] | Task [ 3 ] |
| Sprint | Sprint 16 [ 21 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | Testing In Progress [ 10003 ] |
| Attachment | IGV_ShowTranslation&FlipStrand.png [ 13005 ] |
| Attachment | IGV_SplitScreenReads.PNG [ 13006 ] |
| Sprint | Sprint 16 [ 21 ] |
| Sprint | Sprint 17 [ 22 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Sprint 17 [ 22 ] |
| Sprint | Sprint 18 [ 23 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-592 [ 15664 ] |
| Attachment | IGV_SplitScreenReads.PNG [ 13006 ] |
| Attachment | IGV_ShowTranslation&FlipStrand.png [ 13005 ] |
| Comment |
[ 1) We should take IGV's idea of having a "Show Translation" option in the Sequence axis context menu (see "IGV_ShowTranslation&FlipStrand" screenshot).
IGV also provides an option to select a "Translation Table" for specific organisms. Another idea we should take is their "Flip Strand" action available from the Sequence Axis context menu. This allows a user to switch between visualization of the plus and minus DNA strands. I actually think we should take this even further and have an option to "Display + and - Strands"...then there would be 3 sequence axis viewing options: "+ Strand", "- Strand", or "+ and - Strands" (this visualization of the 2 strands may prove to be very beneficial when teaching genomics to high school or college students. Since DNA actually consists of two strands I believe the visualization of both these strands together would provide a more accurate depiction of a genome). ] |
| Comment |
[ 2) IGV also has a nice visualization option for Paired-End reads (see "IGV_SplitScreenReads" screenshot ).
More information can be found on the IGV User's Guide page here (under the "Split Screen View" section): http://www.broadinstitute.org/igv/AlignmentData ] |
| Summary | Examine other Genome Browsers and brainstorm improvements for IGB | Demo other visualization tools |
| Description |
This story was created to serve as a reminder for the task of examining other genome browsers to gain improvement ideas that can be applied to IGB.
*Genome browser to examine include: -UCSC Genome Browser (most popular) -Jalview -Artemis -Ensemble -IGV -Gbrowse/Jbrowse |
Short list: -UCSC Genome Browser -Jalview -Artemis -IGV -Gbrowse/Jbrowse |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Workflow | classic default workflow [ 15877 ] | Loraine Lab Workflow [ 16418 ] |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 16418 ] | Fall 2019 Workflow Update [ 20561 ] |
| Workflow | Fall 2019 Workflow Update [ 20561 ] | Revised Fall 2019 Workflow Update [ 22766 ] |