Mktrost at 14:03, 23 October 2014

2014-10-23T14:03:50Z

← Older revision		Revision as of 10:03, 23 October 2014
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	See [[QPLOT#Output_files\|QPLOT output documentation]] for more details.		See [[QPLOT#Output_files\|QPLOT output documentation]] for more details.

	== ~~VerifyBamID~~ Tutorial Output ==		== QPLOT Tutorial Output ==

	The VerifyBamID output from the [[Tutorial: GotCloud\| GotCloud Tutorial]] looks like this:		The VerifyBamID output from the [[Tutorial: GotCloud\| GotCloud Tutorial]] looks like this:

Mktrost at 03:47, 25 February 2013

2013-02-25T03:47:36Z

← Older revision		Revision as of 23:47, 24 February 2013
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	Rscript HG00096.qplot.R		Rscript HG00096.qplot.R

	==== [[~~File~~:HG00096.qplot.pdf\|HG00096.qplot.pdf]] ====		==== [[Media:HG00096.qplot.pdf\|HG00096.qplot.pdf]] ====


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	Rscript HG00100.qplot.R		Rscript HG00100.qplot.R

	==== [[~~File~~:HG00100.qplot.pdf\|HG00100.qplot.pdf]] ====		==== [[Media:HG00100.qplot.pdf\|HG00100.qplot.pdf]] ====

Mktrost: Created page with '=Example QPLOT Output= QPLOT produces the following files: * .qplot.R *.qplot.stats See QPLOT output documentation for more details. == VerifyBamID T…'

2013-02-25T03:45:10Z

Created page with '=Example QPLOT Output= QPLOT produces the following files: * *.qplot.R * *.qplot.stats See QPLOT output documentation for more details. == VerifyBamID T…'

New page

=Example QPLOT Output=

QPLOT produces the following files:
* *.qplot.R
* *.qplot.stats

See [[QPLOT#Output_files|QPLOT output documentation]] for more details.

== VerifyBamID Tutorial Output ==

The VerifyBamID output from the [[Tutorial: GotCloud| GotCloud Tutorial]] looks like this:

=== HG00096.qplot.stats ===

<pre>
Stats\BAM /home/mktrost/gotcloudTutorialOut/alignment.recal/HG00096.recal.bam /home/mktrost/gotcloudTutorialOut/tmp/alignment.dedup/HG00096.dedup.bam
TotalReads(e6) 0.02 0.02
MappingRate(%) 99.66 99.66
MapRate_MQpass(%) 99.66 99.66
TargetMapping(%) 0.00 0.00
ZeroMapQual(%) 0.07 0.07
MapQual<10(%) 0.12 0.12
PairedReads(%) 99.55 99.55
ProperPaired(%) 98.38 98.38
MappedBases(e9) 0.00 0.00
Q20Bases(e9) 0.00 0.00
Q20BasesPct(%) 99.41 97.76
MeanDepth 4.70 4.70
GenomeCover(%) 0.50 0.50
EPS_MSE 445.09 26.27
EPS_Cycle_Mean 27.39 27.39
GCBiasMSE 0.01 0.01
ISize_mode 185 185
ISize_medium 187 187
DupRate(%) 1.39 1.39
QCFailRate(%) 0.00 0.00
BaseComp_A(%) 27.5 27.5
BaseComp_C(%) 22.5 22.5
BaseComp_G(%) 22.5 22.5
BaseComp_T(%) 27.5 27.5
BaseComp_O(%) 0.0 0.0
</pre>

=== HG00096.qplot.R ===

The R file starts with:
<pre>
NFiles=2;
colvec=c(1,2);
grid.col='gray';
pchvec=c(1,2);
legend.txt=c('HG00096_recal','HG00096_dedup');
lty.vec=c(1);
pdf(file="", height=12, width=12);
</pre>

Update the
pdf(file="", height=12, width=12);
line to be:
pdf(file="HG00096.qplot.R", height=12, width=12);

Then use Rscript to generate the PDF:
Rscript HG00096.qplot.R

==== [[File:HG00096.qplot.pdf|HG00096.qplot.pdf]] ====

=== HG00100.qplot.stats ===

<pre>
Stats\BAM /home/mktrost/gotcloudTutorialOut/alignment.recal/HG00100.recal.bam /home/mktrost/gotcloudTutorialOut/tmp/alignment.dedup/HG00100.dedup.bam
TotalReads(e6) 0.01 0.01
MappingRate(%) 97.13 97.13
MapRate_MQpass(%) 97.13 97.13
TargetMapping(%) 0.00 0.00
ZeroMapQual(%) 0.19 0.19
MapQual<10(%) 0.26 0.26
PairedReads(%) 99.86 99.86
ProperPaired(%) 93.66 93.66
MappedBases(e9) 0.00 0.00
Q20Bases(e9) 0.00 0.00
Q20BasesPct(%) 93.74 95.70
MeanDepth 2.58 2.58
GenomeCover(%) 0.43 0.43
EPS_MSE 477.21 22.19
EPS_Cycle_Mean 23.98 23.98
GCBiasMSE 0.02 0.02
ISize_mode 388 388
ISize_medium 380 380
DupRate(%) 2.43 2.43
QCFailRate(%) 0.00 0.00
BaseComp_A(%) 28.0 28.0
BaseComp_C(%) 22.2 22.2
BaseComp_G(%) 22.1 22.1
BaseComp_T(%) 27.7 27.7
BaseComp_O(%) 0.0 0.0
</pre>

=== HG00100.qplot.R ===

The R file starts with:
<pre>
NFiles=2;
colvec=c(1,2);
grid.col='gray';
pchvec=c(1,2);
legend.txt=c('HG00100_recal','HG00100_dedup');
lty.vec=c(1);
pdf(file="", height=12, width=12);
</pre>

Update the
pdf(file="", height=12, width=12);
line to be:
pdf(file="HG00100.qplot.R", height=12, width=12);

Then use Rscript to generate the PDF:
Rscript HG00100.qplot.R

==== [[File:HG00100.qplot.pdf|HG00100.qplot.pdf]] ====

Understanding QPLOT output - Revision history

Mktrost at 14:03, 23 October 2014

Mktrost at 03:47, 25 February 2013

Mktrost: Created page with '=Example QPLOT Output= QPLOT produces the following files: * *.qplot.R * *.qplot.stats See QPLOT output documentation for more details. == VerifyBamID T…'

Mktrost: Created page with '=Example QPLOT Output= QPLOT produces the following files: * .qplot.R *.qplot.stats See QPLOT output documentation for more details. == VerifyBamID T…'