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Lots of recent bisulfite runs don't have mitochondrial CpG metric #531

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Metric Name in Database CPG Vs Random (Ratio of average coverage)   CpG meth 
lambdaphage CpG meth mitochondrial  CpG meth nuclear
Metric  cpgvsrandom_ratioofmeans    methlevel_acg_percentage_lambdaphage    methlevel_a
cg_percentage_chrmm methlevel_acg_percentage
Category    004. Bisulfite Conversion Metrics   004. Bisulfite Conversion 
Metrics 004. Bisulfite Conversion Metrics   004. Bisulfite Conversion Metrics
TCGA-BLCA-A1AA-TP-11D-A23D-05-79G7-0.8X 7.01E-01    N/A N/A 44.63
TCGA-BLCA-A1AA-TP-11D-A23D-05-79G7-0.8X 7.68E-01    N/A N/A 44.38
TCGA-BLCA-A1AA-TP-11D-A23D-05-79G7-0.8X 7.91E-01    5E-02   42.24   41.09

Original issue reported on code.google.com by benb...@gmail.com on 27 Jun 2013 at 12:10

GoogleCodeExporter commented 8 years ago 
CpG mitochondrial metric is not calculated for D22UNACXX_3_NIC1254A96 and 
C1TH9ACXX_8_NIC1254A96 because their metric files are missing (not generated by 
the pipeline?)

Original comment by natalia....@gmail.com on 27 Jun 2013 at 8:10

GoogleCodeExporter commented 8 years ago 
Maybe the pipeline is not producing them?

Original comment by natalia....@gmail.com on 19 Jul 2013 at 9:40

GoogleCodeExporter commented 8 years ago 
There was an file naming error when i switched over to yapings tool. I just 
fixed it so hopefully things should be working from this point forward

Original comment by zack...@gmail.com on 23 Jul 2013 at 6:37

GoogleCodeExporter commented 8 years ago 
Could we re-run this on old flowcells?  It's hard to help users with their data 
when the mito methylation is not there.  For instance, I am trying to help 
jones lab:

Metric  flowcell_serial geneusID_sample methlevel_acg_percentage_chrmm  methlevel_
aca_percentage_chrmm    methlevel_gca_percentage_chrmm
786-083 C27BUACXX   KEL656A234  N/A N/A N/A

Original comment by benb...@gmail.com on 31 Jul 2013 at 8:25

GoogleCodeExporter commented 8 years ago 
ok, looking into it.

Original comment by zack...@gmail.com on 31 Jul 2013 at 8:32

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 31 Jul 2013 at 8:32

GoogleCodeExporter commented 8 years ago 
generated chrM.Methlevels. should show up in ECDP on next update.

Original comment by zack...@gmail.com on 1 Aug 2013 at 10:08