/[genomes]/quickload/P_patens_Jan_2018/HEADER.md
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Contents of /quickload/P_patens_Jan_2018/HEADER.md

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Revision 140 - (show annotations)
Fri Jan 1 18:12:10 2021 UTC (6 months, 3 weeks ago) by aloraine
File size: 1722 byte(s)
Add Physcomitrella Jan 2018 v3.3 genome and annotations from Phytozome 318
1 <h1>Physcomitrella patens (moss) January 2018 genome assembly</h1>
2 <body>
3 <p>
4 This directory contains annotation and sequence data files from the Physcomitrella patens genome version 3.3 genome released in January 2018. 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.
15 </li>
16 <li>
17 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>.
18 </li>
19 <li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file.
20 </li>
21 <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>.)
22 </li>
23 </ul>
24 </p>
25 <p>
26 <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.
27 </p>
28 <p>
29 To get faToTwoBit and twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
30 </body>

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