This directory contains the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1)), as well as repeat annotations and GenBank sequences. The Feb. 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ Note on chrM: Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as "chrM" in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS, http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq) in the next human assembly release. Files included in this directory: chromAgp.tar.gz - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.tar.gz - 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. 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 files (one file per chromosome). RepeatMasker was run with the -s (sensitive) setting. Using: Jan 29 2009 (open-3-2-7) version of RepeatMasker and RELEASE 20090120 of library RepeatMaskerLib.embl chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED 5+ format (one file per chromosome). hg19.2bit - contains the complete hg19 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. See also: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ est.fa.gz - Human 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 - 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 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. hg19.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 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/hg19/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/hg19/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/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 All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 20-Mar-2009 09:02 538K chromFa.tar.gz 20-Mar-2009 09:21 905M chromFaMasked.tar.gz 20-Mar-2009 09:30 477M chromOut.tar.gz 20-Mar-2009 09:03 163M chromTrf.tar.gz 20-Mar-2009 09:30 7.6M est.fa.gz 16-Jul-2017 11:26 1.5G est.fa.gz.md5 16-Jul-2017 11:26 44 hg19.2bit 08-Mar-2009 15:29 778M hg19.chrom.sizes 08-Mar-2009 14:56 1.9K md5sum.txt 29-Jul-2009 10:04 457 mrna.fa.gz 16-Jul-2017 11:03 275M mrna.fa.gz.md5 16-Jul-2017 11:03 45 refMrna.fa.gz 16-Jul-2017 11:27 67M refMrna.fa.gz.md5 16-Jul-2017 11:27 48 upstream1000.fa.gz 16-Jul-2017 11:28 8.9M upstream1000.fa.gz.md5 16-Jul-2017 11:28 53 upstream2000.fa.gz 16-Jul-2017 11:29 17M upstream2000.fa.gz.md5 16-Jul-2017 11:29 53 upstream5000.fa.gz 16-Jul-2017 11:29 42M upstream5000.fa.gz.md5 16-Jul-2017 11:29 53 xenoMrna.fa.gz 16-Jul-2017 11:15 5.8G xenoMrna.fa.gz.md5 16-Jul-2017 11:16 49 xenoRefMrna.fa.gz 16-Jul-2017 11:27 235M xenoRefMrna.fa.gz.md5 16-Jul-2017 11:27 52