Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 8.5.0 Major Release
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Labels:
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Story Points:3
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Epic Link:
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Sprint:Sprint 29
Description
Ivory has mentioned that the output of MACS2 includes a file that ends with a .NarrowPeak extension (see attached file).
This file format is currently not supported in IGB. We should add support for this file format in the near future.
Attachments
Issue Links
- is duplicated by
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Link | This issue relates to IGBF-250 [ IGBF-250 ] |
| Sprint | Sprint 10 [ 15 ] |
| Rank | Ranked lower |
| Sprint | Sprint 10 [ 15 ] |
| Rank | Ranked higher |
| Story Points | 3 |
| Sprint | Sprint 12 [ 17 ] |
| Rank | Ranked higher |
| Sprint | Sprint 12 [ 17 ] |
| Rank | Ranked lower |
| Sprint | Sprint 14 [ 19 ] |
| Rank | Ranked higher |
| Sprint | Sprint 14 [ 19 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-165 [ 14687 ] |
| Epic Link | IGBF-165 [ 14687 ] | IGBF-440 [ 15498 ] |
| Rank | Ranked lower |
| Sprint | Backlog Grooming Meeting [ 35 ] |
| Rank | Ranked lower |
| Rank | Ranked lower |
| Sprint | Backlog Grooming Meeting [ 35 ] | Sprint 27 [ 36 ] |
| Sprint | Backlog Grooming [ 36 ] | Sprint 27 [ 35 ] |
| Rank | Ranked lower |
| Sprint | Sprint 27 [ 35 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Summary | Provide support for .NarrowPeak file format | Support for .NarrowPeak file format |
| Rank | Ranked higher |
| Summary | Support for .NarrowPeak file format | Support .NarrowPeak file format |
| Sprint | Sprint 28 [ 36 ] |
| Rank | Ranked lower |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | David Norris [ dcnorris ] | Tarun Mall [ tmall ] |
| Assignee | Tarun Mall [ tmall ] | David Norris [ dcnorris ] |
| Sprint | Sprint 28 [ 36 ] |
| Sprint | Sprint 29 [ 37 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
Before closing this issue, I still want to test some larger files. Ivory may have access to such files.
| Status | Needs Testing [ 10002 ] | Testing Blocked [ 10201 ] |
While testing I noticed that there was a strange "i" letter that was appearing on the narrow peak (see attached screenshot).
This ONLY happens on Mac, not on Windows, and this is ONLY happening on one of the three models from the file.
Reassigning to David to take a deeper look at this issue.
| Assignee | Mason Meyer [ mason ] | David Norris [ dcnorris ] |
| Attachment | testNP.narrowPeak [ 13228 ] | |
| Attachment | letterInNarrowPeak.png [ 13229 ] |
| Status | Testing Blocked [ 10201 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
After reviewing the narrowPeak and broadPeak implementation with Ivory, we think there are a few adjustments that should be made:
1) An unassigned name field in the file is represented by a period. This period is showing as a label above the model in IGB, but since it is just a period it does not look like a label, but rather an odd artifact in the data. Ideally, in the case of a period for the name field, IGB should display something other than a period for the label (something like "NA" or "Unlabeled").
2) The selection info for a narrowPeak file is displaying the CDS start/end info for the peak. This is not what the tooltips for the narrowPeak file shows, so ideally, they should be in sync and show the peak location rather than displaying the ends of the peak as CDS start/end.
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
| Status | Open [ 1 ] | Testing In Progress [ 10003 ] |
It has been decided that point number 2 from the comment above will be addressed in story IGBF-1022. Before working on this story, we must first complete IGBF-1021, which involves refactoring the selection info/tooltips.
Point number 1 from the comment above has been fixed and tested, so this story will now be closed.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Fix Version/s | 8.5.0 Major Release [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | Open [ 1 ] |
| Labels | Data_Provider |
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 15461 ] | Fall 2019 Workflow Update [ 19250 ] |
| Workflow | Fall 2019 Workflow Update [ 19250 ] | Revised Fall 2019 Workflow Update [ 21367 ] |
| Attachment | NarrowPeakTestFile.narrowpeak [ 12864 ] |
Same as old file but with first letter of chromosome names converted to upper-case C
| Attachment | NarrowPeakTestFile.narrowpeak [ 14585 ] |
My testing for this issue included:
-Verifying that narrowPeak and broadPeak files are now supported in IGB.
-Verifying that the label seen in IGB represents the name (field 4) of the data.
-Verifying that the direction of the model seen in IGB is representative of the the strand field (field 6).
-Verifying that the peak (field 10) can be seen in the visualization of the narrowPeak file.