Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#236 closed defect (invalid)

Reporter import of Illumina BGX file fails on section [controls]

Reported by: Jari Häkkinen Owned by: Nicklas Nordborg
Priority: major Milestone:
Component: net.sf.basedb.illumina Keywords:
Cc:

Description

The issue is the same as reported for feature import for array designs (I cannot locate the ticket ... maybe it was reported by email only?). The problem is simply that the number of columns in the [controls] section of Illumina MicroRNA BGX-files only have 5 columns whereas the importer expects 6. A sample BGX is attached to this ticket.

Attachments (1)

humanMI_V2_R0_XS0000124-MAP.bgx (63.7 KB) - added by Jari Häkkinen 12 years ago.

Download all attachments as: .zip

Change History (3)

Changed 12 years ago by Jari Häkkinen

comment:1 Changed 12 years ago by Nicklas Nordborg

Milestone: Illumina package v1.4Illumina package v1.x
Resolution: invalid
Status: newclosed

The ticket you are looking for is #215. The current implementation of that importer was never intented to work with BGX files that doesn't have the following 6 columns in the [Controls] section: Probe_ID, Array_Address_Id, Reporter_Group_Name, Reporter_Group_Id, Reporter_Composite_Map, Probe_Sequence.

If support for the new file format is needed a new set of plug-ins (feature importer, reporter importer) are required.

comment:2 Changed 12 years ago by Jari Häkkinen

Milestone: Illumina package v1.x
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