This directory contains the Dec. 2008 assembly of the zebrafish genome
(danRer6, Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)), as well as repeat annotations and GenBank sequences.
This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
Massachusetts..
For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/
Files included in this directory:
danRer6.agp.gz - Description of how the assembly was generated from
fragments.
danRer6.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
danRer6.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
danRer6.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)
danRer6.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
danRer6.2bit - contains the complete danRer6 Zebrafish Genome
in the 2bit format. A utility program, twoBitToFa (available
from our src tree), can be used to extract .fa file(s) from
this file. See also:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
est.fa.gz - Zebrafish ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Zebrafish mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq data which is updated daily for most assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
danRer6.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/danRer6/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
Name Last modified Size Description
Parent Directory -
danRer6.2bit 2009-07-06 13:41 381M
danRer6.agp.gz 2009-07-08 13:37 1.5M
danRer6.chrom.sizes 2009-06-24 14:41 188K
danRer6.fa.gz 2009-07-08 13:59 463M
danRer6.fa.masked.gz 2009-07-08 14:04 240M
danRer6.fa.out.gz 2009-07-08 13:48 117M
danRer6.trf.bed.gz 2009-07-08 13:49 9.1M
est.fa.gz 2019-10-16 23:52 305M
est.fa.gz.md5 2019-10-16 23:52 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2010-01-25 15:41 463
mrna.fa.gz 2019-10-16 23:36 18M
mrna.fa.gz.md5 2019-10-16 23:36 45
refMrna.fa.gz 2019-10-16 23:53 12M
refMrna.fa.gz.md5 2019-10-16 23:53 48
upstream1000.fa.gz 2019-10-16 23:54 4.1M
upstream1000.fa.gz.md5 2019-10-16 23:54 53
upstream2000.fa.gz 2019-10-16 23:54 7.9M
upstream2000.fa.gz.md5 2019-10-16 23:54 53
upstream5000.fa.gz 2019-10-16 23:54 19M
upstream5000.fa.gz.md5 2019-10-16 23:54 53
xenoMrna.fa.gz 2019-10-16 23:46 6.8G
xenoMrna.fa.gz.md5 2019-10-16 23:46 49
xenoRefMrna.fa.gz 2019-10-16 23:53 319M
xenoRefMrna.fa.gz.md5 2019-10-16 23:53 52