/[genomes]/quickload/D_discoideum_Ax4_May_2009/HEADER.md
ViewVC logotype

Contents of /quickload/D_discoideum_Ax4_May_2009/HEADER.md

Parent Directory Parent Directory | Revision Log Revision Log


Revision 23 - (show annotations)
Thu Sep 27 13:58:58 2018 UTC (2 years, 6 months ago) by aloraine
File size: 2066 byte(s)
Add Dictyostelim discoideum (slime mold) May 2009 assembly and annotations, from DictyDB
1 <html>
2 <title>Slime mold QuickLoad data directory</title>
3 <body>
4 <h2>
5 Slime mold QuickLoad data directory
6 </h2>
7 <p>
8 This directory contains annotation files for the slime mold
9 Dictyostelium discoideum strain Ax4 genome that was available as of
10 May, 2009. Ann Loraine (of the <a
11 href="http://www.transvar.org">Loraine Lab</a>) created all the files
12 you see here using GFF files obtained in July 2010 from the <a
13 href="http://www.dictybase.org/Downloads/"> dictyBase file Download
14 section</a>.
15 </p>
16 <p>
17 To access these data in Integrated Genome Browser, launch IGB (see:
18 <a href="http://www.bioviz.org/igb">bioviz.org/igb</a>) and
19 choose species Dictyostelium discoideum Ax4 and then genome version
20 D_discoideum_Ax4_May_2009 in the Data Access Panel.
21 (For documentation about IGB, see <a href="http://wiki.transvar.org/confluence/display/igbman/Home">The IGB User's Guide</a>.)
22 </p>
23 <p>
24 All the available data files you see in this directory
25 should appear in the Data Sources section of the Data Access panel. If you want to load
26 everything all at once into several tracks, choose ALL and then choose Load Mode
27 Whole Genome under the Load Mode section of the Data Access Panel. The Dicty genome is
28 a very manageable size, and so we highly recommend you load everything all at once!
29 </p>
30 <p>
31 To view genomic sequence, zoom in and click Load Sequence in View or Load All Sequence. The
32 latter will load all the sequence for the current chromsome. Since this genome is quite
33 small, we highly recommend the Load All Sequence option.
34 </p>
35 <p>
36 To load next-gen sequencing data from sorted, indexed BAM files, just click-drag them
37 from your desktop or a server into the IGB interface. The same goes for "bar" (tiling
38 array) files.
39 </p>
40 <p>
41 We gratefully acknowledge Siddhartha Basu of Northwestern University and
42 <a href="http://www.dictybase.org/About_dictyBase/">the
43 dictyBase Team</a> for helping us set up this Dicty QuickLoad site. Thank you
44 and we look forward to working with you in future!
45 </p>
46 <p>
47 Sincerely,<br/>
48 The Loraine Lab IGB team
49 </p>
50 </body>
51 </html>

  ViewVC Help
Powered by ViewVC 1.1.26