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Commit 112f0326 authored by tjc's avatar tjc
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addiotonal docs for analyses etc

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16350 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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...@@ -3,7 +3,8 @@ ...@@ -3,7 +3,8 @@
<PARA> <PARA>
&prog; can read in and visualise BAM, VCF and BCF files. These files need &prog; can read in and visualise BAM, VCF and BCF files. These files need
to be indexed as described below. They require &prog; to be run with at least to be indexed as described below. They require &prog; to be run with at least
Java 1.6. Java 1.6. Some examples can be found on the
<ULINK URL="http://www.sanger.ac.uk/resources/software/artemis/ngs/">Artemis homepage</ULINK>.
</PARA> </PARA>
<PARA> <PARA>
<ULINK URL="http://samtools.sourceforge.net/">BAM</ULINK> files need to be sorted and indexed using <ULINK <ULINK URL="http://samtools.sourceforge.net/">BAM</ULINK> files need to be sorted and indexed using <ULINK
...@@ -12,7 +13,32 @@ the same directory as the BAM file. This provides an integrated ...@@ -12,7 +13,32 @@ the same directory as the BAM file. This provides an integrated
<ULINK URL="http://bamview.sourceforge.net/">BamView</ULINK> panel in &prog;, displaying <ULINK URL="http://bamview.sourceforge.net/">BamView</ULINK> panel in &prog;, displaying
sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded
in from here either by selecting each file individually or by selecting a file of in from here either by selecting each file individually or by selecting a file of
path names to the BAM files. path names to the BAM files. The BAM files can be read from a local file system or remotely
from an HTTP server.
</PARA>
<PARA>
BamView will look to match the length of the sequence in Artemis with the reference sequence lengths
in the BAM file header. It will display a warning when it opens if it finds a matching reference sequence
(from these lengths) and changes to displaying the reads for that. The reference sequence for the mapped
reads can be changed manually in the drop down list in the toolbar at the top of the BamView.
</PARA>
<PARA>
In the case when the reference sequences are concatenated together into one (e.g. in a multiple
FASTA sequence) and the sequence length matches the sum of sequence lengths given in the
header of the BAM, Artemis will try to match the names (e.g. locus_tag or label) of the
features (e.g. contig or chromosome) against the reference sequence names in the BAM. It will
then adjust the read positions accordingly using the start position of the feature.
</PARA>
<PARA>
When open the BamView can be configured via the popup menu which is activated by clicking on the
BamView panel. The 'View' menu allows the reads to be displayed in a number of views: stack,
strand-stack, paired-stack, inferred size and coverage.
</PARA>
<PARA>
In Artemis the BamView display can be used to calculate the number of reads mapped to the
regions covered by selected features. In addition the reads per kilobase per million mapped reads (RPKM)
values for selected features can be calculated on the fly. Note this calculation can take
a while to complete.
</PARA> </PARA>
<PARA> <PARA>
Variant Call Format (<ULINK Variant Call Format (<ULINK
...@@ -61,5 +87,10 @@ alternative colouring schemes. It is possible to colour the variants by whether ...@@ -61,5 +87,10 @@ alternative colouring schemes. It is possible to colour the variants by whether
synonymous or non-synonymous or by their quality score (the lower the quality the synonymous or non-synonymous or by their quality score (the lower the quality the
more faded the variant appears). more faded the variant appears).
</PARA> </PARA>
<PARA>
Filtered data can be exported in VCF format, or the reconstructed DNA sequences of variants
can be exported in FASTA format for selected features or selected regions for further analyses.
These sequences can be used as input for multiple sequence alignment tools.
</PARA>
</SECT2> </SECT2>
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