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Fix ErrorRate calculation in upload_summary_values.pl #10

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cbrumme opened this issue Sep 8, 2014 · 0 comments
Open

Fix ErrorRate calculation in upload_summary_values.pl #10

cbrumme opened this issue Sep 8, 2014 · 0 comments
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@cbrumme
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cbrumme commented Sep 8, 2014

On Lines 201-222 of upload_summary_values.pl:

The script is currently trying to calculate the average ErrorRate over the first 35 bases of each read. The SQL queries as written don't calculate the correct value.
Regardless, we would rather track the average ErrorRate over the entire read (not just the first 35 bases)

I believe the following SQL will do that:

READ 1

$query = "SELECT AVG(errorRate) from specimen.MiSeqQC_ErrorMetrics WHERE runID LIKE ". $RunID." AND ". $read1

READ 2

$query = "SELECT AVG(errorRate) from specimen.MiSeqQC_ErrorMetrics WHERE runID LIKE ". $RunID." AND ". $read2

see lines 59-62 for the definitions of $read1 and $read2

@cbrumme cbrumme added the bug label Sep 8, 2014
@donkirkby donkirkby added this to the near future milestone Apr 14, 2015
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