Details
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Type:
Bug
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
Description
I made a bigbed file from the pollen junctions file (see image).
This looks like the separate exons are not preserved (but that information is in the file). And the strand information is not preserved. IGB is showing all features on the + strand, but I'm not sure if the file format has lost the information or if IGB is simply not reading the information correctly, and therefore is not displaying it correctly.
Main task here is to investigate the parsing and displaying of bigbed files and create jira tasks/bug reports for items that should be fixed.
Steps to make this bigbed file:
- in R (could also use awk or sed) - bedToBigBed does not tolerate scores above 1000
p = read.delim("Pollen.bed", header=F)
p$V5=0
write.table(p, "Pollen.noScore.bed", sep="\t", col.names=F, row.names=F, quote=F)
- bash
bedToBigBed Pollen.noScore.bed genomeC.txt PollenJuncs.noScore.bb
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Workflow | Loraine Lab Workflow [ 17964 ] | Fall 2019 Workflow Update [ 18853 ] |
| Workflow | Fall 2019 Workflow Update [ 18853 ] | Revised Fall 2019 Workflow Update [ 20978 ] |
| Status | Open [ 1 ] | To-Do [ 10305 ] |