Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Fixed
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Labels:None
Description
- open H sapiens
- Save, then drag in the IGIS Gene Models.GFF file (attached. Make sure to save the .tbi file to the same location as the main file.).
- zoom in until you have 1/2 of a gene showing on screen (make sure the other half is out of the field of view)
- hit load data. See that the IGIS models loaded.
- now zoom out, you will see the IGIS models end at the black and sometimes a single line extends into the grey, unloaded area. The exons on the ends are not showing.
- while zoomed out, hit Load Data again
this test passes if the rest of the exons load onto the 'parent' line. This fails if they are drawn as a new line
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Lance Frohman [ lfrohman ] |
| Attachment | IGIS Gene Models.gff.gz.tbi [ 11050 ] | |
| Attachment | IGIS Gene Models.gff.gz [ 11051 ] |
| Assignee | Lance Frohman [ lfrohman ] | Hiral Vora [ hiralv ] |
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Attachment | image.png [ 11052 ] | |
| Attachment | image 2.png [ 11053 ] | |
| Description |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see #1 below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see #2 below) |
| Description |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see #1 below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see #2 below) |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see image 2.png below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see image.png below) |
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Description |
- H sapiens - Open the IGIS Gene Models.GFF file. - you need to zoom into a region so that there is a gene that extends beyond the visible zoom region on both sides on the refseq (the IGIS file is very similar to refseq) - hit load data - now zoom out, you will see the exons on the ends are not showing - if you hit Load Data again, some show and some do not. Steps 1) - select h sapiens - delete refseq - open file IGIS... - select view mode default - region "chr1 : 111,733,948 - 111,735,852" - load data (nothing shows) - region "chr1 : 111,728,298 - 111,744,083" - load data (see image 2.png below) 2) - select h sapiens - delete refseq - open file IGIS... - select view mode default - (leave full region for chr1) - load data - region "chr1 : 111,728,298 - 111,744,083" (this is how it should look, see image.png below) |
- open H sapiens - Save, then drag in the IGIS Gene Models.GFF file (attached. Make sure to save the .tbi file to the same location as the main file.). - zoom in until you have 1/2 of a gene showing on screen (make sure the other half is out of the field of view) - hit load data. See that the IGIS models loaded. - now zoom out, you will see the IGIS models end at the black and sometimes a single line extends into the grey, unloaded area. The exons on the ends are not showing. - while zoomed out, hit Load Data again this test passes if the rest of the exons load onto the 'parent' line. This fails if they are drawn as a new line |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Summary | GFF file does not show correctly | Indexed GFF file does not partial load correctly |
| Reporter | Lance Frohman [ lfrohman ] | Alyssa Gulledge [ alyssa ] |
| Attachment | partial.model.png [ 11759 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Richard Linchangco [ richard ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Richard Linchangco [ richard ] | Alyssa Gulledge [ alyssa ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Assignee | Alyssa Gulledge [ alyssa ] |
| Attachment | PARTIAL.png [ 11765 ] | |
| Attachment | FULL.png [ 11766 ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |