This directory contains the v.1.0 Mmul_051212 rhesus genome assembly (rheMac2, Jan. 2006) produced by the Baylor College of Medicine Human Genome Sequencing Center. For more information about these data, see the Baylor web page at http://www.hgsc.bcm.tmc.edu/projects/rmacaque/. Files included in this directory: rheMac2.2bit - contains the complete rhesus/rheMac2 genome sequence in the 2bit file format. 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. The utility program, twoBitToFa (available from the kent src tree), can be used to extract .fa file(s) from this file. A pre-compiled version of the command line tool can be found at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html est.fa.gz - Rhesus macaque ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - Rhesus macaque 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. chromFa.tar.gz - The assembly sequence in one file per chromosome. Repeats from RepeatMasker and Tandem Repeats Finder are shown in lower case; non-repeating sequence is shown in upper case. RepeatMasker 19 Jan 2006 version with RepBase libraries: RepBase Update 9.11, RM database version 20060120. NOTE: In most assemblies, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the lower case masking includes all repeats. chromFaMasked.tar.gz - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.tar.gz - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.tar.gz - Tandem Repeats Finder locations, translated into one .bed file per chromosome. NOTE: In most assemblies, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so these files contain all Tandem Repeats Finder results. rheMac2.agp.tar.gz - Description of how the assembly was generated from fragments. rheMac2.qual.qv.gz - base by base qual scores for rheMac2 assembly. Values vary from 0 to 60. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for RefSeq genes with annotated 5' UTRs. This file is updated weekly so it could 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. v1.edit3.noContam.ctg.fasta.gz - The unmasked contigs fasta from the assembly. v1.edit3.noContam.ctg.qv.gz - The per base quality scores from contigs sequences. v1_edit4.scf.fasta.gz - The sequences for the large scaffolds that were using in the assembly. rheMac2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/rheMac2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) Please review the restrictions on the use of the rhesus assembly data at http://genome.ucsc.edu/goldenPath/credits.html#rhesus_use.
Name Last modified Size Description
Parent Directory - chromFa.tar.gz 2006-06-12 15:13 832M chromFaMasked.tar.gz 2006-06-12 15:20 457M chromOut.tar.gz 2006-06-12 14:31 143M chromTrf.tar.gz 2006-06-12 14:31 13M est.fa.gz 2019-10-17 19:15 15M est.fa.gz.md5 2019-10-17 19:15 44 md5sum.txt 2014-01-27 15:37 846 mrna.fa.gz 2019-10-17 19:00 139M mrna.fa.gz.md5 2019-10-17 19:00 45 refMrna.fa.gz 2019-10-17 19:15 4.1M refMrna.fa.gz.md5 2019-10-17 19:15 48 rheMac2.2bit 2006-01-30 18:00 712M rheMac2.agp.tar.gz 2006-02-09 06:49 17M rheMac2.chrom.sizes 2006-02-15 18:06 333 rheMac2.fa.gz 2020-01-23 02:25 833M rheMac2.qual.qv.gz 2006-03-09 13:08 215M upstream1000.fa.gz 2019-10-17 19:16 1.6M upstream1000.fa.gz.md5 2019-10-17 19:16 53 upstream2000.fa.gz 2019-10-17 19:16 3.0M upstream2000.fa.gz.md5 2019-10-17 19:16 53 upstream5000.fa.gz 2019-10-17 19:16 7.2M upstream5000.fa.gz.md5 2019-10-17 19:16 53 v1.edit3.noContam.ctg.fasta.gz 2006-01-27 13:21 830M v1.edit3.noContam.ctg.qv.gz 2006-01-27 13:23 287M v1_edit4.scf.fasta.gz 2006-01-27 15:11 814M xenoMrna.fa.gz 2019-10-17 19:10 6.6G xenoMrna.fa.gz.md5 2019-10-17 19:11 49 xenoRefMrna.fa.gz 2019-10-17 19:15 327M xenoRefMrna.fa.gz.md5 2019-10-17 19:15 52