src/hg/makeDb/trackDb/ntSeqContigs.html 1.1
1.1 2010/05/06 19:43:46 angie
Migrated Neandertal track descriptions from genome-nt.
Index: src/hg/makeDb/trackDb/ntSeqContigs.html
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+<H2>Description</H2>
+<P>
+The Neandertal Sequence Contigs track shows consensus contigs
+called (after duplicate reads from each library were merged) from
+overlapping, non-redundant reads that passed mapping and base
+quality criteria.
+</P>
+
+<H2>Display Conventions and Configuration</H2>
+<P>
+The contigs (query sequences) from each of the six samples are contained in separate
+subtracks. Use the checkboxes to select which samples will be
+displayed in the browser. Click and drag the sample name to reorder the
+subtracks. The order in which the subtracks appear in the subtrack list will
+be the order in which they display in the browser.
+<P>
+The query sequences in the SAM/BAM alignment representation
+are normalized to the + strand of the reference genome
+(see the <A HREF="http://samtools.sourceforge.net/SAM1.pdf#page=4"
+TARGET=_blank>SAM Format Specification</A>
+for more information on the SAM/BAM file format). If a query sequence was
+originally the reverse of what has been stored and aligned, it will have the
+following
+<A HREF="http://samtools.sourceforge.net/SAM1.pdf#page=5"
+TARGET=_blank>flag</A>:
+<PRE>
+(0x10) Read is on '-' strand.
+</PRE></P>
+<P>
+BAM/SAM alignment representations also have <A HREF="http://samtools.sourceforge.net/SAM1.pdf#page=6"
+TARGET=_blank>tags</A>. Some tags are predefined and others (those beginning
+with X, Y or Z) are defined by the aligner or data submitter.
+The following tag is associated with this track:
+<UL>
+<LI><A HREF="http://samtools.sourceforge.net/SAM1.pdf#page=7"
+TARGET=_blank><B>AS</B></A>: Alignment score generated by aligner</LI>
+</UL>
+</P>
+<P>
+The item labels and display
+colors of features within this track can be configured through the controls at
+the top of the track description page.
+</P>
+<UL>
+<LI><B>Display Read Names</B>: By default, read names are not displayed. To
+display the read names, select the check box next to "Display read names".</LI>
+
+<LI><B>Minimum alignment quality</B>: Excludes alignments with quality less than
+the given number. The default is 0.</LI>
+
+<LI><B>Color track by bases</B>: By default, mismatching bases are highlighted
+in the display. Change the selection to "item bases" to see all base
+values from the query sequence, or "OFF" to ignore query sequence.
+Click <A HREF="../../goldenPath/help/hgBaseLabel.html">here</A>
+for additional information.</LI>
+
+<LI><B>Alignment Gap/Insertion Display Options</B>: Click
+<A HREF="../../goldenPath/help/hgIndelDisplay.html">here</A> for help with
+these options.
+
+<LI><B>Additional coloring modes</B>: Other aspects of the alignments can be
+displayed in color or grayscale.</LI>
+ <UL>
+ <LI><B>Color by strand</B>: Alignments on the reverse strand are colored
+ dark red, alignments on the forward strand are colored dark blue.</LI>
+
+ <LI><B>Grayscale</B>: Items are shaded according to the chosen method:
+ alignment quality or base qualities. The alignment qualities of individual
+ items are shaded on a scale of 0 (lightest) to 99 (darkest).
+ Base qualities are shaded on a scale of 0 (lightest) to 40 (darkest).
+ Alignment quality is the default.</LI>
+ </UL>
+ </LI>
+</UL>
+</P>
+
+<H2>Methods</H2>
+<P>
+All Neandertal sequence reads from each of the six samples were aligned
+to the $organism ($db) genome using the short read aligner/mapper
+<A HREF="http://bioinf.eva.mpg.de/anfo" TARGET=_blank>ANFO</A>.
+</P>
+<P>
+To reduce the effects of sequencing error, the alignments of Neandertal reads to
+the human and chimpanzee reference genomes were used to construct human-based
+and chimpanzee-based consensus "minicontigs". To generate the consensus,
+uniquely placed, overlapping alignments were selected (ANFO MAPQ ≥ 90) and
+these were merged into a single multi-sequence alignment using the common
+reference genome sequence.
+</P>
+<P>
+At each position in the resulting alignment, for each observed base, and for
+each possible original base: i) The likelihood of the observation was
+calculated, ii) the likely length of single-stranded overhangs was estimated,
+and iii) the potential for ancient DNA damage using the Briggs-Johnson model was
+considered (Briggs <EM>et al</EM>. 2007).
+If most observations in a given position showed a gap, the consensus became a
+gap; otherwise the base with the highest quality score (calculated by dividing
+each likelihood by the total likelihood) was used as the consensus.
+</P>
+<P>
+At the current coverage, heterozygous sites will appear as low quality bases
+with the second base (not shown) having a similar likelihood to the consensus
+base.
+Likewise, heterozygous indels are included only by chance or may show up as
+stretches of low quality bases.
+</P>
+
+<H2>Credits</H2>
+<P>
+This track was produced at UCSC using data generated by
+<A HREF="mailto:ed@soe.ucsc.edu"
+title="ed@soe.ucsc.edu" rel="nofollow"
+TARGET = _BLANK>Ed Green</a>.
+</P>
+
+<H2>Reference</H2>
+<P>Briggs AW, <EM>et al</EM>.
+<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/17715061"
+TARGET=_blank>Patterns of damage in genomic DNA sequences from a Neandertal</A>.
+<EM>Proc Natl Acad Sci USA</EM>. 2007. Sep 11;104(37):14616-21.
+</P>
+<P>
+Green RE, <EM>et al.</EM> A Draft Sequence of the Neandertal Genome.
+<EM>Science</EM>. 2010 (Accepted).
+</P>