@@ -110,18 +110,23 @@ Thus, an example settings configuration is as follows:
}
~~~
#### Example configurations
In most cases, it's practical to combine the samples and settings configuration into one file. Here is an [example config file](/examples/gentrap_example.json) where both samples and settings are stored into one file. Note also that there are additional tool configurations in the config file.
## Running Gentrap
As with other pipelines in the Biopet suite, Gentrap can be run by specifying the pipeline after the `pipeline` subcommand:
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
#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.
#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
The following plot shows basic <a href="https://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Alignment">alignment</a> statistics for this run. Every sample 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.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
#if (sampleId.isDefined && libId.isDefined)
something
#elseif(sampleId.isDefined)
This plot shows the insert size distribution for the libraries of sample ${sampleId}. <a href="http://thegenomefactory.blogspot.nl/2013/08/paired-end-read-confusion-library.html">Insert size</a> denotes the size of the so-called <em>insert</em> between two read pairs in a paired-end sequencing run. This should correspond to the length of the sequence between the sequencing adaptors. The provided table shows mean and median insert size for each sample, together with the standard deviation.
#else
This plot shows the insert size distribution for each of the ${samples.size} samples. <a href="http://thegenomefactory.blogspot.nl/2013/08/paired-end-read-confusion-library.html">Insert size</a> denotes the size of the so-called <em>insert</em> between two read pairs in a paired-end sequencing run. This should correspond to the length of the sequence between the sequencing adaptors. The provided table shows mean and median insert size for each sample, together with the standard deviation.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
Here we show the total number of positions in the reference that are covered with a given coverage. This plot is whole-genome based, and will therefore be highly skewed in the case of an exome or targeted approach.