/[genomes]/quickload/M_acuminata_DH_Pahang_Jan_2016/HEADER.md
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Revision 37 - (show annotations)
Thu Sep 27 14:47:45 2018 UTC (3 years, 9 months ago) by aloraine
File size: 2210 byte(s)
Add Musa acuminata DH Pahang (Jan 2016) banana (v2) genome assembly and annotations
1 <h1>Banana genome assembly</h1>
2 <body>
3
4 <p> This directory contains annotation and sequence data files from
5 the banana Musa acuminata DH Pahang version 2 genome assembly released January 2016. Files
6 are formatted for visualization in <a href="https://bioviz.org/">Integrated Genome Browser</a> (IGB).
7 </p>
8
9 <p>
10 Files include:
11 </p>
12 <p>
13 <ul>
14 <li>
15 2bit file - sequence file in two-bit format, created using
16 faToTwoBit.
17 When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
18 To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
19 </li>
20 <li>
21 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>.
22
23 <li>genome.txt - meta-data file listing 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>
24
25 <li>reference gene model annotations 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>.)
26 </ul>
27 </p>
28 <p>
29 <b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB.
30 </p>
31 <p>Gene model annotation file(s) include:
32 <ul>
33 <li>M_acuminata_DH_Pahang_Jan_2016.bed.gz - gene models downloaded in GFF3 format from the <a href="http://banana-genome-hub.southgreen.fr/download">Banana Genome Hub download page</a> and converted to IGB-friendly format (BED-detail) using gff3ToBedDetail.py from this <a href="https://bitbucket.org/lorainelab/genomesource">git repository</a>.
34 </li>
35 </ul>
36 <p>
37 For more information about quickload, visit <a href="https://bioviz.org">bioviz.org</a> and visit the on-line, searchable IGB User's Guide.
38 </p>
39 </body>

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