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: Fixed
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Labels:None
Description
Open a BAM file; do not load sequence. Open sliced view. Zoom in until you can see the actual sequence on the reads. Double click/select a read that is in a relatively deep stack (>20 reads) but set the read depth to 10. There is a very good chance that the selected read does NOT appear in the sliced view because it gets incorporated into the summary/collapsed line of reads that the top of the frame. Also notice that the reads showing in the zoomed in main view are NOT the same set of reads being shown in the sliced view - all of this is due to read packing.
Sourceforge# 3046549
**editted to refine the problem (original issue was that the sequence of a selected read is not appearing in the sliced view.)
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Status | Open [ 1 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Afshan Jalali [ afshan ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Katharine Kubiak [ kkubiak ] |
I cannot reproduce this bug.
The link does not work, so I tried to test with other BAM files. When I set the horizontal zoom all the way to the right then load the BAM file, it is a blank screen. When I open sliced view, it is a blank screen.
| Assignee | Katharine Kubiak [ kkubiak ] | Alyssa Gulledge [ alyssa ] |
| Summary | Read sequences don't appear in sliced view | Bam Read packing issue: Selected read (identified by sequence) doesn't appear in sliced view because the reads pack differently in the sliced view |
| Description |
1. Open IGB; Arabidopsis thaliana, Jun_2009 2. Load a sample BAM file from http://www.bioviz.org/quickload/A_thaliana_Jun_2009/nextgen_samples/ 3. Set the horizontal zoom to the far right BEFORE loading the BAM file. 4. Character sequences can be seen in the view. 5. Click on the Sliced view. 6. The character sequences should appear in the "sliced view" also, as they appear in the upper view. Sourceforge# 3046549 Testing Results: Sept 30, 2010 - Alyssa Gulledge version 6.4 (6969) This bug is still present. The sliced view does NOT show the GATC sequence that can be seen in the upper window. |
Open a BAM file; do not load sequence. Open sliced view. Zoom in until you can see the actual sequence on the reads. Double click/select a read that is in a relatively deep stack (>20 reads) but set the read depth to 10. There is a very good chance that the selected read does NOT appear in the sliced view because it gets incorporated into the summary/collapsed line of reads that the top of the frame. Also notice that the reads showing in the zoomed in main view are NOT the same set of reads being shown in the sliced view - all of this is due to read packing. Sourceforge# 3046549 **editted to refine the problem |
| Description |
Open a BAM file; do not load sequence. Open sliced view. Zoom in until you can see the actual sequence on the reads. Double click/select a read that is in a relatively deep stack (>20 reads) but set the read depth to 10. There is a very good chance that the selected read does NOT appear in the sliced view because it gets incorporated into the summary/collapsed line of reads that the top of the frame. Also notice that the reads showing in the zoomed in main view are NOT the same set of reads being shown in the sliced view - all of this is due to read packing. Sourceforge# 3046549 **editted to refine the problem |
Open a BAM file; do not load sequence. Open sliced view. Zoom in until you can see the actual sequence on the reads. Double click/select a read that is in a relatively deep stack (>20 reads) but set the read depth to 10. There is a very good chance that the selected read does NOT appear in the sliced view because it gets incorporated into the summary/collapsed line of reads that the top of the frame. Also notice that the reads showing in the zoomed in main view are NOT the same set of reads being shown in the sliced view - all of this is due to read packing. Sourceforge# 3046549 **editted to refine the problem (original issue was that the sequence of a selected read is not appearing in the sliced view.) |
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
| Assignee | Hiral Vora [ hiralv ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Katharine Kubiak [ kkubiak ] |
Find a gene where there are about 20 reads deep, set max depth to 10. Select (highlight) a read in the visible stack. Zoom in to about 1 exon wide image. NOW open sliced view. Sliced view did/does repack just the visible reads, and this can cause the selected read to move 'up' into the summary reads, or just significantly move location within the stack of reads.
The fix would be to NOT permit sliced view to repack - repack should only happen in main view.
Passed Windows v12138
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Katharine Kubiak [ kkubiak ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
I cannot reproduce this bug.