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<h1>Physcomitrella patens (moss) January 2018 genome assembly</h1> <body> <p> 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). </p> <p> Files include: </p> <p> <ul> <li> 2bit file - sequence file in two-bit format, created using faToTwoBit. When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. </li> <li> 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>. </li> <li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. </li> <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>.) </li> </ul> </p> <p> <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. </p> <p> To get faToTwoBit and twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>. </body>
Name | Last modified | Size | Description | |
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Parent Directory | - | |||
annots.xml | 2023-06-16 14:09 | 353 | Annotation and data file list | |
genome.txt | 2023-06-16 14:09 | 6.7K | Chromosome lengths and assembly information | |
P_patens_Jan_2018.bed.gz.tbi | 2023-06-16 14:09 | 72K | Tabix index file | |
P_patens_Jan_2018.bed.gz | 2023-06-16 14:09 | 3.7M | Annotation or junction file | |
P_patens_Jan_2018.2bit | 2023-06-16 14:09 | 113M | Sequence data in blat 2bit format |