__EXCLUSIVE__ Download Mm10 Reference Genome
Zerihun Tanoesoedibjo
Search the assembly:
- By position or search term: Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. More information, including sample queries.
- By gene name: Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. More information.
- By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.
mm10 has been updated with patches since its release in 2012. GRC patch releases do not change anypreviously existing sequences; they simply add new sequences for fix patches or alternate haplotypesthat correspond to specific regions of the main chromosome sequences. For most users, the patchesare unlikely to make a difference and may complicate the analysis as they introduce moreduplication. The UCSC mm10 patch level 6 contains 9 alternate scaoffolds from the reference strain C57BL/6J.
- chr1_KK082441_alt
- chr11_KZ289080_alt
- chr11_KZ289074_alt
- chr11_KZ289078_alt
- chr11_KZ289081_alt
- chr11_KZ289079_alt
- chr11_KZ289075_alt
- chr11_KZ289073_alt
- chr11_KZ289077_alt It also contains 99 alternate scaffolds from 14 other mouse strains which are included in the NCBIrelease GRC MM38.
The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability. Drosophia melanogaster experiments are mapped to either dm3 or dm6 and Caenorhabdilis elegans experiments are mapped to ce10 or ce11. The official reference files for each Uniform processing pipeline can be found in the table below, organized by organism and pipeline. In addition to the genome sequences (we generally use the "no alt" version for each genome), a variety of other crucial files can be found there as well (GENCODE transcript references, chromosome size files, the phage lambda genome, etc.).
The table below includes files used by each pipeline for uniform processing by the ENCODE DCC, with associated details on genome assembly and annotation, if applicable. For your convenience, the GRC genome assembly and GENCODE annotation files are directly linked below. For further information, please contact encod...@lists.stanford.edu
Some of the experiments at the ENCODE portal have not been processed by the DCC uniform processing pipelines and may have used different reference files. The References search page includes all the reference datasets used by the different projects whose data could be found on the portal.
While GRCm38 from NCBI is technically the same build (in terms of sequence content), the sequence identifiers will differ between the original at NCBI and what UCSC produces. Then ERCC RNA data is an extra layer of annotation added to base genomes available at certain sources (GEO and Ensembl host these, I believe, and perhaps others). The source mm10 from UCSC used at Galaxy Main does not include this content.
If you wish to use a different genome version for mouse than what is available at Galaxy Main, a local/cloud Galaxy can be used with a genome added with a Data Manager (from any source) or you can try using the Custom Genome feature at Galaxy Main - just be aware that using such a large genome as a custom genome may create jobs that run out of memory.
To be clear, in practical terms, the start coordinate format (0-based or 1-based) is dependent on the datatype of the dataset/file. This is independent of the underlying version of the reference genome.
The workflow you are using is inputting the reference genome as a custom reference genome from the history during execution. This is one way to do the analysis. Another is to install reference genome indexes on the server you are working on (if your own or you can make requests). And the final way is to use the built-in native indexes on the server you are working on.
It looks as if you are working on Galaxy Main If so, then both mm10 and hg38 are natively indexed for most tools on the server. This means that you do not need to upload the reference genome to your history. And it increases the chance of a successful job as these larger genomes can quickly use up resources building a new index each run. You will need to modify the workflow so that tools use the built-in indexes instead of a custom reference genome.
How to use a Custom reference genome (and where to potentially source one, example: UCSC) is explained in the last link here. Also review the Chromosome mismatch FAQ at this location - all inputs must be based on the exact same reference genome or problems will come up with tools/results.
I am doing an RNA-seq experiment and I ran HiSAT2 with the mm10 reference genome. Then in order to run htseq-count I downloaded grcm38 gtf file from Ensembl. The only gtf file in the galaxy database is mm9. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the gene_id attribute incorrectly contains the same value as the transcript_id attribute". Htseq-count results in all reads counts in the "no features" file. Presumably because I ran HiSAt2 with mm10 and htseq-count with grcm38?
So should I go back and run HiSAT2 with grcm38 reference genome? If so, how do I get the grcm38 hisat2 reference index into Galaxy?I tried to download the grcm38 index from the HiSAT2 webpage and I got a folder with about 10 files "genome.2.ht2, genome.3.ht2" for example. There is also a script in the folder called "make_grcm38.sh". When I run this script in that directory, it returns the error "Could not find hisat2-build in current directory or in PATH".
Please try the Gencode GTF version of the annotation. It contains chromosome identifiers that are a match for UCSC's mm10. Avoid the GFF3 version - it will have less utility and some RNA-seq tools will not accept GFF3 annotation as input, or they might error due to the content not meeting a strict GFF3 specification.
You can load this into Galaxy by copy/pasting the URL to the Upload tool. Set the metadata datatype to gtf and database to mm10 so that tools recognize it as an appropriate/matched input for other mm10 input dataset(s).
The BAM should have mm10 already assigned if created with HISAT2 in Galaxy -- yet assign if needed (uploaded BAM). Galaxy cannot autodetect database during Upload - it must be set by the user or the external data source (not all do this).
My question is that I read most of the mouse sequence paper, there is no one use mm10 as reference for alignment, and seems like mm10 has fewer annotation compared with mm9, is that true? Has anyone use mm10 for alignment and get a good result?
mm10 annotation will catch up eventually. There was a similar issue with the human genome; hg19 used to be much less complete compared with hg18 but now most people have moved to hg19. It's just a function of when you start work compared with time since last release in the build cycle.
mm10 is better for alignment based (more reads are mapped) on personal experience. Also, it has been a while since mm10 is out so its the right time to make the transition. All the gene models including UCSC, RefSeq and Ensembl are available for mm10. And for other annotations you can always liftOver mm9 to mm10.
Is there a kind soul that could take me through a step-by-step of fetching and indexing the mouse mm10 genome from UCSC (or wherever) on a local galaxy install, with a data manager? I have the indexers installed as well as create db key, rsync, and fetch reference genome. I just can't seem to make this work. I've also tried indexing a locally cached mm10 reference genome with the hisat indexer, but hisat2 can't seem to use it (see error description in my other post).
Your screenshot of the finder showing the genomes directory seems to be of your main igv directory, not the IGVTools directory. I just tried downloading igvtools from and the info required for mm10 was there. Did you move the igvtools.jar to the main igv directory and run it from there? If so, it is trying to pick up the genome from the igv/genomes directory, not from the IGVTools/genomes directory. The igv/genomes directory will not necessarily have all the genomes, as its contents depend on which genomes you have used with the IGV desktop application.
Hello! I am currently trying to use one of the built-in reference genomes, mm10, in the GenomicDistributionsData package to make different plots from the GenomicDistributions package for my own analysis. From testing out the example here ( -genomic-range-data), everything worked fine if I used the hg19 genome. The problem came when I tried to change the genome to "mm10" like so:
From the GenomicDistributionsData Bioconductor documentation and example HTML, I tried running the following lines to see if mm10 was present in the list of genomes/genome parts, but what returned was "character(0) ":
You need to give more information about what happened when you ran calcChromBinsRef rather than what you did to try to diagnose (for example, there are no datasets in the GenomicDistributionData package - it just helps find data on the ExperimentHub). Anyway, calcChromBinsRef will call getChromSizes, which needs a BSGenome package for mm10 to work. R probably told you something after you tried to run calcChromBinsRef but you don't say what that was. Without that information we can only guess. You want to provide enough information so we don't have to do that.
The iGenomes are a collection of reference sequences and annotation files for commonly analyzed organisms. The files have been downloaded from Ensembl, NCBI, or UCSC. Chromosome names have been changed to be simple and consistent with the download source. Each iGenome is available as a compressed file that contains sequences and annotation files for a single genomic build of an organism.
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