src/hg/makeDb/trackDb/ntSeqReads.html 1.1
1.1 2010/05/06 19:43:46 angie
Migrated Neandertal track descriptions from genome-nt.
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+<H2>Description</H2>
+<P>
+The Neandertal Seq track shows Neandertal sequence reads mapped to the $organism
+genome. The Neandertal sequence was generated from six Neandertal fossils found
+in Croatia, Germany, Spain and Russia.
+</P>
+
+<H2>Display Conventions and Configuration</H2>
+<P>
+The sequence reads (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>
+<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, selected 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>
+The Neandertal sequence was genereated from six Neandertal fossils. Vi33.16
+(54.1% genome coverage), Vi33.25 (46.6%) and Vi33.26 (45.2%) were discovered in
+the Vindija cave in Croatia. Feld1 (0.1%) is from the Neandertal type specimen
+from the Neander Valley in Germany, Sid1253 (0.1%) is from El Sidron cave in
+Asturias, Spain, and Mez1 (2%) is from Mezmaiskaya in the Altai Mountains,
+Russia.</P>
+<P>
+To increase the fraction of endogenous Neandertal DNA in the sequencing
+libraries, restriction enzymes were used to deplete libraries of microbial DNA.
+This was done by identifying Neandertal sequencing reads whose best alignment
+was to a primate sequence, and selecting enzymes that would differentially cut
+non-primate fragments. These enzymes all contained CpG dinucleotides in their
+recognition sequences, reflecting the particularly low abundance of this
+dinucleotide in mammalian DNA. Sequencing was carried out on the 454 FLX and
+Titanium platforms and the Illumina GA. Neandertal reads were mapped to the
+$organism genome ($db) using a custom mapper called
+<A HREF="http://bioinf.eva.mpg.de/anfo"
+title="http://bioinf.eva.mpg.de/anfo" TARGET=_blank>ANFO</A>. This custom
+alignment program was developed to take into account the characteristics of
+ancient DNA. Following the observation and implementation by Briggs
+<EM>et al</EM>., ANFO
+uses different substitution matrices for DNA thought to be double-stranded
+versus single-stranded and changes between them if doing so affords a better
+score.
+</P>
+
+<H2>Credits</H2>
+<P>
+This track was produced at UCSC with data generated by
+<A HREF="mailto:ed@soe.ucsc.edu"
+title="ed@soe.ucsc.edu" rel="nofollow"
+TARGET = _BLANK>Ed Green</a>.
+</P>
+
+<H2>References</H2>
+<P>
+Briggs AW, <em>et al</em>.
+<A HREF="http://www.sciencemag.org/cgi/content/abstract/325/5938/318"
+TARGET=_blank>Targeted retrieval and analysis of five Neandertal mtDNA
+genomes</A>. <EM>Science</EM>. 2009 Jul 17;325(5938):318-21.</P>
+<P>
+Green RE, <EM>et al.</EM> A Draft Sequence of the Neandertal Genome.
+<EM>Science</EM>. 2010 (Accepted).
+</P>