/[genomes]/quickload/M_domestica_Borkh_Jun_2017/HEADER.md
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Revision 38 - (hide annotations)
Thu Sep 27 14:50:39 2018 UTC (4 years ago) by aloraine
File size: 1961 byte(s)
Add Malus domestica Borkh (GDDH13 Version 1.1) apple genome assembly and annotations
1 aloraine 38 <h1>Malus domestica (apple) June 2017 genome assembly</h1>
2     <body>
3     <p>
4     This directory contains annotation and sequence data files from the GDDH13 Version 1.1 apple genome released in June 2017. Files are formatted for visualization in <a href="https://bioviz.org">Integrated Genome Browser</a> (IGB).
5     </p>
6     <p>
7     Files include:
8     </p>
9     <p>
10     <ul>
11     <li>
12     2bit file - sequence file in two-bit format, created using
13     faToTwoBit.
14     When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
15     To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
16     </li>
17     <li>
18     annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="https://bioviz.org">Integrated Genome Browser</a>.
19    
20     <li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>
21    
22     <li>reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: <a href="http://bioinformatics.oxfordjournals.org/content/27/5/718">Tabix: fast retrieval of sequence features from generic TAB-delimited files</a> and <a href="http://genome.ucsc.edu/FAQ/FAQformat.html">http://genome.ucsc.edu/FAQ/FAQformat.html</a>.)
23     <li>sub-directories with additional data, including mRNA and EST alignments, RNA-Seq data sets, etc.
24     </ul>
25     </p>
26     <p>
27     <b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. Gene model annotation files use BED-detail format, which is the same as BED12 but contains two additional fields: field 13 contains the locus identifier and field 14 contains descriptive text.
28     </p>
29     </body>

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