Details
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Type:
Bug
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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: 8.5.3 Minor Release
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Labels:
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Story Points:0.5
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Sprint:Sprint 32
Description
There currently is no way to change the default behavior of only counting "single-mapping reads" - these are reads with NH attribute equal to "1"
In the older version of FindJunctions, you could set this.
Also, the parameter name "threshold" is a bit confusing.
1) In the FindJunctions window, change "threshold" parameter to "flank"
2) Change the default behavior to using all reads, not just the singly mapped (NH = 1) reads.
3) Ensure that if a user has a applied a filter to a track, only the reads that pass the filter get used as inputs to FindJunctions
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
From Ann:
In IGB 8.5 - and also some earlier versions - the IGB FindJunctions track operation lists parameter "threshold." I think this is actually the parameter listed as "flank" in the command-line version of the program. This is the number of bases that a splice read has to cover on either side of putative junction in order to be counted as support. Also, there is now no way to change the default behavior of only counting "single-mapping reads" - these are reads with NH attribute equal to "1" In the older version of FindJunctions, you could set this. However, this is also OK -- provided a user can use filters to get single-mapping behavior if they want. *To resolve this issue we need to: - change "treshold" parameter to "flank" and make sure this is right - change default behavior to NOT use single-mapping reads - ensure that if a user has a applied a filter to a track, only the reads that pass the filter get used as inputs to FindJunctions |
There currently is no way to change the default behavior of only counting "single-mapping reads" - these are reads with NH attribute equal to "1"
In the older version of FindJunctions, you could set this. Also, the parameter name "threshold" is a bit confusing. 1) In the FindJunctions window, change "threshold" parameter to "flank" 2) Change the default behavior to using all reads, not just the singly mapped (NH = 1) reads. 3) Ensure that if a user has a applied a filter to a track, only the reads that pass the filter get used as inputs to FindJunctions |
| Story Points | 0.5 |
| Assignee | David Norris [ dcnorris ] |
| Sprint | Sprint 30 [ 38 ] |
| Sprint | Sprint 31 [ 39 ] |
| Rank | Ranked higher |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
| Sprint | Sprint 31 [ 39 ] |
| Sprint | Sprint 32 [ 40 ] |
| Rank | Ranked higher |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
This issue was tested during an IGB meeting on 2/9/2016. The issue seems to be working as expected so the issue will now be closed.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 8.5.3 Minor Release [ 10202 ] |
| Summary | FindJunctions track operation not working as expected | Find Junctions Only Counting Single-mapping reads |
| Labels | Track_Operators |
This issue has been retested for the 8.5.3 minor release and it is good to go.
| Workflow | Loraine Lab Workflow [ 16698 ] | Fall 2019 Workflow Update [ 19722 ] |
| Workflow | Fall 2019 Workflow Update [ 19722 ] | Revised Fall 2019 Workflow Update [ 21841 ] |
I have completed 1 and 2. #3 is already implemented as the default behavior.