Physcomitrella patens (moss) January 2018 genome assembly

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 Integrated Genome Browser (IGB).

Files include:

• 2bit file - sequence file in two-bit format, created using faToTwoBit. When users click Load Sequence buttons, IGB retrieves sequence data from this file.
• annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into Integrated Genome Browser.
• genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file.
• reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: Tabix: fast retrieval of sequence features from generic TAB-delimited files and http://genome.ucsc.edu/FAQ/FAQformat.html.)

Note: 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.

To get faToTwoBit and twoBitInfo, visit http://hgdownload.cse.ucsc.edu/admin/exe/.

	Name	Last modified	Size	Description
	Parent Directory		-
	annots.xml	2023-06-16 14:09	353	Annotation and data file list
	P_patens_Jan_2018.bed.gz	2023-06-16 14:09	3.7M	Annotation or junction file
	genome.txt	2023-06-16 14:09	6.7K	Chromosome lengths and assembly information
	P_patens_Jan_2018.2bit	2023-06-16 14:09	113M	Sequence data in blat 2bit format
	P_patens_Jan_2018.bed.gz.tbi	2023-06-16 14:09	72K	Tabix index file