Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#675 closed defect (fixed)

Running a mask/align job as debug for a non-debug demux doesn't change the outcome

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

Description

The help text for the debug option says:

When running in debug mode only part of the sequenced data is used and temporary files are not removed from the cluster node.

While the last part is true, the first part is not, since it assumes that the demuxed data has been created with debug as well.

Change History (3)

comment:1 by Nicklas Nordborg, 10 years ago

I think there are two things that should be fixed:

  • Add -u parameter to bowtie in the first step. This should automatically limit the input to tophat.
  • Add 'debug' suffix to the data files directory so that debug runs are not mixed up with real runs.

comment:2 by Nicklas Nordborg, 10 years ago

Resolution: → fixed
Status: new → closed

(In [2848]) Fixes #675: Running a mask/align job as debug for a non-debug demux doesn't change the outcome

comment:3 by Nicklas Nordborg, 10 years ago

(In [2849]) References #675: Running a mask/align job as debug for a non-debug demux doesn't change the outcome

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