Opened 6 years ago

Closed 6 years ago

#641 closed task (fixed)

Import data from cufflinks result files

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v2.17
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

When Cufflinks has completed it has created isoforms.fpkm_tracking and some other files. The data from the file should be imported as raw data to a raw bioassay in BASE. Before this can be done we need to have some information already in the database (eg. reporters and an array design).

Change History (8)

comment:1 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 6 years ago by Nicklas Nordborg

(In [2723]) References #641: Import data from cufflinks result files

Change BASE dependency to 3.2.2 since we need to install configurations for some of the BASE core plug-ins. See http://base.thep.lu.se/ticket/1859.

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [2724]) References #641: Import data from cufflinks result files

Install configurations for importing reporters and array design features from GTF files and raw data from cufflinks isoforms.fpkm_tracking files.

The configurations all use standard BASE core plug-ins and use <transcript_id> as the reporter id and feature id. So far, only the minimal number of columns are imported but this is expected to change when all details has been set.

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [2725]) References #641: Import data from cufflinks result files

Schedules a raw data import job from the 'isoforms.fpkm_tracking' file when Cufflinks has completed. Seems to work as expected.

comment:5 Changed 6 years ago by Nicklas Nordborg

(In [2747]) References #641: Import data from cufflinks result files

Adding configuration files for adding reporter annotation columns and raw data columns for cufflinks.

Reporter columns: refseq, protAcc Cufflinks columns: locus, length

Updated import plug-in configurations to import to the new columns.

Installation instructions updated since it is now a lot more complicated to get everything installed correctly.

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [2851]) References #641: Import data from cufflinks result files

chromosome property is enabled by default in reggie extended properties since it is better to get an error message about duplicate definition when installing that at a later time when trying to import data to a missing property.

comment:7 Changed 6 years ago by Nicklas Nordborg

(In [2856]) References #641: Import data from cufflinks result files

reggie-ogs-hosts.xml is no longer in root directory.

comment:8 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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