Commit 3e309603 authored by Wai Yi Leung's avatar Wai Yi Leung

Rewrite a bit on a sentence about "depending"

parent 957aa6c5
......@@ -28,7 +28,7 @@
#if (sampleId.isDefined && libId.isDefined)
Here we show basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for sample ${sampleId} with library ${libId}. Total number of reads, number of alignments reads and number of duplicate reads are given, and the percentages thereof as a percentage of total.
#elseif(sampleId.isDefined && showPlot)
The following plot shows basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for sample ${sampleId}. Every library is represented by a multi-color bar. Red represents the total number of properly mapped reads for this sample. Green represents the total number of duplicates reads, which is usually caused by <a href="http://www.cureffi.org/2012/12/11/how-pcr-duplicates-arise-in-next-generation-sequencing/">PCR duplicates</a>. Blue denotes the number of unmapped reads, and purple denotes reads flagged <em>secondary</em> (this is dependent on the aligner used). A table showing similar statistics, including values represented as percent of total, can be downloaded as a tab-delimited file.
The following plot shows basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for sample ${sampleId}. Every library is represented by a multi-color bar. Red represents the total number of properly mapped reads for this sample. Green represents the total number of duplicates reads, which is usually caused by <a href="http://www.cureffi.org/2012/12/11/how-pcr-duplicates-arise-in-next-generation-sequencing/">PCR duplicates</a>. Blue denotes the number of unmapped reads, and purple denotes reads flagged <em>secondary</em> (this depends on the aligner used). A table showing similar statistics, including values represented as percent of total, can be downloaded as a tab-delimited file.
#elseif(sampleId.isDefined && !showPlot)
Here we show basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run for every library of sample ${sampleId}. Total number of reads, number of alignments reads and number of duplicate reads are given, and the percentages thereof as a percentage of total.
#else
......
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