#1347 closed enhancement (fixed)

Updates to registration of specimen handled by external lab

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.33.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

See #1295 for background.

New features:

  • R1size and R2size entries in the fastq section that can be used to verify that the complete FASTQ files have been transfered.
  • Library/Plate well entry is now specifying coordinates using A:1 format. Update It was not just a formatting issue. The 'A:1' format is used when the library prep is made on 8x12 plates and the '1:1' format is used when the library prep is made on 1x8 strips. The plate format is going to be used in the normal workflow, but there may be situations when the strip format is used instead. We should model this and introduce a "LibStrip?" plate type with 1x8 geometry. We can use the format of the Library/Plate well value to decide which plate type to use.
  • New value in Library/Protocol: TruSeq Stranded mRNA - Expression - Breast. The ExternalRef annotation for the corresponding library protocol need to be updated manually in lorry.

Change History (14)

comment:1 Changed 13 months ago by Nicklas Nordborg

In 6457:

References #1347: Updates to registration of specimen handled by external lab

Implemented support for checking FASTQ file size.

comment:2 Changed 13 months ago by Nicklas Nordborg

In 6458:

References #1347: Updates to registration of specimen handled by external lab

Fixes a NullPointerException if the SCANB_ID entry is missing.

comment:3 Changed 13 months ago by Nicklas Nordborg

In 6459:

References #1347: Updates to registration of specimen handled by external lab

The changes in [6457] and [6458] was committed to the trunk but they should have been in the reggie/4.33-stable branch. This update merge the same changes to the reggie/4.33-stable
branch.

comment:4 Changed 13 months ago by Nicklas Nordborg

In 6460:

References #1347: Updates to registration of specimen handled by external lab

Added support for plate coordinates in "A:1" format.

comment:5 Changed 13 months ago by Nicklas Nordborg

In 6462:

References #1347: Updates to registration of specimen handled by external lab

Added a column for showing the number of reads in the FASTQ files.

comment:6 Changed 13 months ago by Nicklas Nordborg

In 6463:

References #1347: Updates to registration of specimen handled by external lab

Increasing the warning limit about library size to 500.

comment:7 Changed 13 months ago by Nicklas Nordborg

Description: modified (diff)

comment:8 Changed 13 months ago by Nicklas Nordborg

In 6464:

References #1347: Updates to registration of specimen handled by external lab

Added new plate type "External library strip" and new geometry "1x8".

comment:9 Changed 13 months ago by Nicklas Nordborg

In 6465:

References #1347: Updates to registration of specimen handled by external lab

The library importer will now select the plate type depending on the format of the Plate well value. If the value is digit:digit the STRIP_1x8 is selected otherwise the PLATE_8x12.

comment:10 Changed 13 months ago by Nicklas Nordborg

In 6466:

References #1347: Updates to registration of specimen handled by external lab

Make the FASTQ file size easer to read by using a thousands separator.

comment:11 Changed 13 months ago by Nicklas Nordborg

In 6467:

References #1347: Updates to registration of specimen handled by external lab

Figure out which FASTQ is R1 and which is R2 by checking the stored annotation values instead of using the find command. The pattern used may not always match.

comment:12 Changed 13 months ago by Nicklas Nordborg

In 6468:

References #1347: Updates to registration of specimen handled by external lab

Use the number of reads in the FASTQ files to set the READS annotation.

comment:13 Changed 13 months ago by Nicklas Nordborg

In 6469:

References #1347: Updates to registration of specimen handled by external lab

Changing the soft warning limits for the number of reads and improving the display by adding thousand separators.

comment:14 Changed 13 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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