This directory contains the Build 36.1 finished human genome assembly (hg18, Mar. 2006). The chromosomal sequences were assembled by the International Human Genome Project sequencing centers. Files included in this directory: chromAgp.zip - Description of how the assembly was generated, unpacking to one file per chromosome. chromFa.zip - The assembly sequence in one file per chromosome. 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. Repeat masking was done using the following RepeatMasker/RepBase versions: RepBase Update 9.11, RM database version 20050112. The main assembly is found in the chrN.fa files, where N is the name of the chromosome. The chrN_random.fa files contain clones that are not yet finished or cannot be placed with certainty at a specific place on the chromosome. In some cases, including the human HLA region on chromosome 6, the chrN_random.fa files also contain haplotypes that differ from the main assembly. chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromOut.RM3.2.7.zip - RepeatMasker (v3.2.7) .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period of less than or equal to 12, and translated into one .bed file per chromosome. contigAgp.zip - Description of how the assembly was generated from fragments at a contig layout level. contigFa.zip - The assembly sequence contigs, in one file per NCBI contig. All contigs are in forward orientation relative to the chromosome. In some cases, this means that contigs will be reversed relative to their orientation in the NCBI assembly. Repeats from RepeatMasker and Tandem Repeats Finder are shown in lower case; non-repeating sequence is shown in upper case. contigFaMasked.zip - The assembly sequence contigs, in one file per contig. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. contigOut.zip - RepeatMasker .out file for contigs. These were created by RepeatMasker at the -s sensitive setting. contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per contig. hg18.2bit - hg18.2bit contains the complete hg18 Human 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. hg18.RM.tbl.tar.gz - the RepeatMasker .tbl file output. Each file in this tar file is for one chunk of contig sequence used during the RepeatMasker operation, for example: 1/NT_004321/NT_004321_0.fa.tbl There are 5990 of these chunks of contig sequences, their coordinate coorrespondence to contig coordinates can be found in the hg18.RM.lft.tar.gz lift files. hg18.RM.lft.tar.gz - lift files to lift the hg18.RM.tbl coordinates to contig coordinates. est.fa.gz - Human ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. liftAll.zip - Offsets of contigs within chromosomes. mrna.fa.gz - Human 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 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.zip - Same as upstream1000, but 2000 bases. upstream5000.zip - 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. ----------------------------------------------------------------- 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 hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/hg18/bigZips 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. All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory - chromAgp.zip 2006-04-06 09:45 537K chromFa.zip 2006-02-03 11:05 899M chromFaMasked.zip 2006-02-03 11:12 487M chromOut.RM3.2.7.zip 2009-02-05 10:10 162M chromOut.zip 2006-02-03 10:51 153M chromTrf.zip 2006-02-03 11:35 6.8M contigAgp.zip 2006-02-03 11:12 596K contigFa.zip 2006-02-03 11:27 898M contigFaMasked.zip 2006-02-03 11:35 488M contigOut.zip 2006-02-03 11:14 152M contigTrf.zip 2006-02-03 11:35 7.0M est.fa.gz 2019-10-17 06:40 1.5G est.fa.gz.md5 2019-10-17 06:40 44 hg18.2bit 2005-12-20 10:33 770M hg18.RM.lft.tar.gz 2008-11-10 14:08 41K hg18.RM.tbl.tar.gz 2008-11-10 13:55 1.3M hg18.chrom.sizes 2005-12-06 16:34 855 liftAll.zip 2006-02-03 11:35 5.5K md5sum.txt 2009-02-05 10:25 734 mrna.fa.gz 2019-10-17 06:22 370M mrna.fa.gz.md5 2019-10-17 06:22 45 refMrna.fa.gz 2019-10-17 06:41 80M refMrna.fa.gz.md5 2019-10-17 06:41 48 upstream1000.fa.gz 2019-10-17 06:42 9.4M upstream1000.fa.gz.md5 2019-10-17 06:42 53 upstream2000.fa.gz 2019-10-17 06:43 18M upstream2000.fa.gz.md5 2019-10-17 06:43 53 upstream5000.fa.gz 2019-10-17 06:43 46M upstream5000.fa.gz.md5 2019-10-17 06:43 53 xenoMrna.fa.gz 2019-10-17 06:31 6.4G xenoMrna.fa.gz.md5 2019-10-17 06:32 49 xenoRefMrna.fa.gz 2019-10-17 06:41 250M xenoRefMrna.fa.gz.md5 2019-10-17 06:41 52