This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phastCons124way/README.txt
This directory contains compressed phastCons scores for
multiple alignments of 123 genome sequences on the reference
D. melanogaster/dm6/Aug. 2014 assembly.
See also: assemblyInformation.txt for information about which
assemblies have been used in this 124-way multiple alignment
Files in this directory:
md5sum.txt - MD5 checksums to verify download files
dm6.124way.phastCons/*.wigFix.gz - scores in fixed step wiggle format
dm6.phastCons124way.mod - phastCons tree model for the 124 species
dm6.phastCons124way.bw - scores in bigWig format:
nameCrossReference.txt - tab separated columns with the different names
- for these sequences and databases, columns:
1. sequence name - UCSC database or scientific name
- sequence names used in MAF files
2. NCBI accession
3. NCBI taxon identifier
4. assembly name
5. scientific name
assemblyInformation.txt - summary listing of each sequence used
See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
for bigWig format description
For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
The phyloP data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP124way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz124way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm6&g=cons124way
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Note, the uncompressed *.wigFix.gz files are 706 Mb of data, when compressed,
they are approximately 121 Mb of compressed data. The entire set of
data in this directory is approximately 371 Mb.
To download a large file or multiple files from this directory, we recommend
that you use rsync or ftp rather than downloading the files via our website.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/phastCons124way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/dm6/phastCons124way
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Use the "prompt" command to toggle the interactive mode if you do not want
to be prompted for each file that you download.
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All the files in this directory are freely available for public use.
For data use restrictions regarding the genome assemblies used in this
annotation, see http://genome.ucsc.edu/goldenPath/credits.html.
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References for phastCons and phyloP:
Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates
on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
(http://genome.cshlp.org/content/20/1/110.long)
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson
H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements
in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005
Aug;15(8):1034-50. (http://genome.cshlp.org/content/15/8/1034.full)
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Name Last modified Size Description
Parent Directory -
nameCrossReference.txt 2018-11-28 09:37 8.7K
dm6.124way.phastCons/ 2018-11-28 14:31 -
assemblyInformation.txt 2018-11-28 16:46 14K
dm6.phastCons124way.mod 2018-12-20 12:45 4.6K
dm6.phastCons124way.bw 2018-12-20 14:29 250M
md5sum.txt 2018-12-21 11:48 230