Opened 2 months ago

Last modified 8 days ago

#1159 new enhancement

Release exporter changes due to MIPs pipeline

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.23
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The first task is to make sure that existing items in the RNA-seq pipeline are exported as expected and that no "contamination" is happening from items in the MIPs pipeline. It is not expected that contamination should happen but I still think that some queries should at least have a filter to really make sure that items from the correct pipeline are loaded.

The second task is to define what should be exported from the MIPs pipeline. We already have the DNA items and then we probably need the Library items and MergedSequences items. What is below that is not yet known. Most likely we need to export different annotations for items in the MIPs pipeline.

Change History (3)

comment:1 Changed 2 weeks ago by Nicklas Nordborg

In 5549:

References #1159: Release exporter changes due to MIPs pipeline

The release exporter plug-in has been updated to also export child Library items to DNA.

The RNA path path requires that the pipeline annotation is set to RNAseq on the library items, and the DNA path that the pipeline annotation is set to MIPs.

So far the MIPs libraries are exported with the same information as the RNAseq libraries except for concentration-related annotations since this is not measured. No MIPs specific annotations are exported (but the could be moved down from the normalized DNA aliquot if desired).

comment:2 Changed 2 weeks ago by Nicklas Nordborg

In 5550:

References #1159: Release exporter changes due to MIPs pipeline

Updated to include merged items belonging to the MIPs pipeline. Annotations related to Trimmomatic and fragment sizes are not included since those steps are not performed (we should maybe add other annotations once the demux for MIPs has been settled). FASTQ files are exported, including the UMI file.

comment:3 Changed 8 days ago by Nicklas Nordborg

In 5576:

References #1159: Release exporter changes due to MIPs pipeline

Exporting the "Pipeline" annotation also for raw bioassays.

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