Why chrMT? The assembly hg19 has two mitochondrial genomes, chrM (old) and chrMT (current). The reason is that for hg19, no mitochondrial sequence was in the GRCh37 sequence file. The UCSC Genome Browser originally added a chrM sequence when making hg19 that was not the mitochondrial genome sequence later selected by NCBI for GRCh37. This is why the current hg19 version contains two mitochondrial sequences, the old one called "chrM" and the current GRCh37 reference, called "chrMT". The issue is described in detail in our - + hg19 sequence download instructions. If you use hg19 today, chrMT should be considered the current mitochondrial sequence, chrM is only supported for backwards compatibility and legacy annotation files. Our hg19.fa.gz in the "current" download directory contains both sequences, the old hg19.fa.gz in the top level download directory has only chrM, for backwards compatibility for old pipelines and our analysisSet fasta file for aligners contains only chrMT. For most purposes when using hg19, we recommend using the analysis set fasta file.
For hg38, there is no issue, it has only chrM, and all mitochondrial annotations are present on chrM.
UCSC Genes on hg19: For hg19, the knownCanonical table is a subset of the UCSC Genes track. It was generated at UCSC by identifying a canonical isoform for each cluster ID, or gene. Generally, this is the longest isoform. It can be downloaded directly from the hg19 downloads database +href="http://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/">hg19 downloads database or by using the Table Browser.
Gencode on hg38/mm10 - knownCanonical: For hg38, the knownCanonical table is a subset of the GENCODE v29 track. It was generated at UCSC. As opposed to the hg19 knownCanonical table, which used computationally generated gene clusters and generally chose the longest isoform as the canonical isoform, the hg38 table uses ENSEMBL gene IDs to define clusters (that is to say, one canonical isoform per ENSEMBL gene ID), and the method of choosing the isoform is described as such:
knownCanonical identifies the canonical isoform of each cluster ID or gene using the ENSEMBL gene IDs to define each cluster. The canonical transcript is chosen using the APPRIS principal transcript when available. If no APPRIS tag exists for any transcript associated with the cluster, then a transcript in the BASIC set is chosen. If no BASIC transcript exists, then the longest isoform is used.
It can be downloaded directly from the hg38 downloads database +href="http://hgdownload.gi.ucsc.edu/goldenPath/hg38/database/">hg38 downloads database or by using the Table Browser.
NCBI RefSeq (hg19/hg38): This track collection contains three subtracks that select the most relevant transcript for all or a subset of genes, with slightly different aims:
We provide files in GTF format, which is an extension to GFF2, for most assemblies. More information on GTF format can be found in our FAQ.
These files are generated for four gene model tables: ncbiRefSeq, refGene, ensGene, knownGene. Certain assemblies, such as hg19, will have all four files while smaller assemblies may only have one or two of these. Which file a user should use depends on their analysis, as they contain different data and metadata.
These files are generated using the genePredToGtf method described in our
downloads FAQ using the -utr flag. They can be found on the download server
-address http://hgdownload.soe.ucsc.edu/goldenPath/$db/bigZips/genes/ where
+address http://hgdownload.gi.ucsc.edu/goldenPath/$db/bigZips/genes/ where
$db is the assembly of interest. For example, the hg38 GTF files.
The best approach to get protein-coding genes out of GENCODE is to join data with a related attributes table, and specifically name the desired biotype(s).
Here is an introductory example using the Public MySQL server to access the wgEncodeGencodeBasicV39 table of all genes and the wgEncodeGencodeAttrsV39 related table to find the transcriptType for each entry and to select those that are annotated as protein-coding genes. There are a number of biotypes that can be accessed by looking at the table scheme and clicking the values link for the transcriptType field. These terms are also more fully described on the GENCODE biotypes page. The example below will attempt to make a simple example to select all types that have "protein_coding" in this transcriptType field:
-mysql -u genome -h genome-mysql.soe.ucsc.edu hg38 -e 'select g.name,a.transcriptType from wgEncodeGencodeBasicV39 g, wgEncodeGencodeAttrsV39 a where (g.name = a.transcriptId) and (a.transcriptType = "protein_coding");' +mysql -u genome -h genome-mysql.gi.ucsc.edu hg38 -e 'select g.name,a.transcriptType from wgEncodeGencodeBasicV39 g, wgEncodeGencodeAttrsV39 a where (g.name = a.transcriptId) and (a.transcriptType = "protein_coding");'
What this query does is access the hg38 database, and then from the wgEncodeGencodeBasicV39 table, it takes the name field (g.name) and looks in the related wgEncodeGencodeAttrsV39 table for a matching transcriptId field (g.name = a.transcriptId), and then screens for only entries in wgEncodeGencodeAttrsV39 that are equal to protein-coding (a.transcriptType = "protein_coding"). In this way selecting all the entries which are annotated as protein-coding. Please note this selection will return some of the unusual protein-coding cases that one would not consider, for instance, it will return genes one may not want (or want), such as Immunoglobulin and T-cell receptor components.
For the manually curated RefSeq gene set, transcript identifiers start with NM_ for coding or NR_ for non-coding, followed by a number and version number separated by a dot, e.g. "NR_046018.2" for an RNA pseudogene. For RefSeq one can select coding genes by filtering for NM identifiers. On the concept of genes, it may be worth noting that the @@ -830,31 +830,31 @@ and miRNA (microRNA), hinting at the abundant types of RNA molecules.
Since there are many different kinds of non-coding elements in GENCODE, a better step for non-coding selection is to join data with a related attributes table, and specifically name a specific desired biotype or biotypes, such as only lncRNAs. There are a number of biotypes that can be accessed by looking at the table scheme and clicking the values link for the transcriptType field. These terms are also more fully described on the GENCODE biotypes page.
Here is an introductory example using the Public MySQL server to access the wgEncodeGencodeBasicV39 table of all genes and the wgEncodeGencodeAttrsV39 related table to find the transcriptType for each entry and to select just lncRNA entries.
-mysql -u genome -h genome-mysql.soe.ucsc.edu hg38 -e 'select g.name,a.transcriptType from wgEncodeGencodeBasicV39 g, wgEncodeGencodeAttrsV39 a where (g.name = a.transcriptId) and (a.transcriptType = "lncRNA");' +mysql -u genome -h genome-mysql.gi.ucsc.edu hg38 -e 'select g.name,a.transcriptType from wgEncodeGencodeBasicV39 g, wgEncodeGencodeAttrsV39 a where (g.name = a.transcriptId) and (a.transcriptType = "lncRNA");'
What this query does is access the hg38 database, and then from the wgEncodeGencodeBasicV39 table, it takes the name field (g.name) and looks in the related wgEncodeGencodeAttrsV39 table for a matching transcriptId field (g.name = a.transcriptId), and then screens for only entries in wgEncodeGencodeAttrsV39 that are equal to lncRNA (a.transcriptType = "lncRNA"). In this way selecting all of these types, which again, may not be the only subset desired. By modifying the above query, it is possible to add further qualifiers and generate a subset of different non-coding elements meeting specific research needs.
For the manually curated RefSeq gene set, transcript identifiers start with NM_ for coding or NR_ for non-coding, followed by a number and version number separated by a dot, e.g. "NR_046018.2" for an RNA pseudogene. For RefSeq, one can select non-coding genes by filtering for NR identifiers. Note that a pseudogene of mRNA is not an unambiguous concept, and there may be a desire to look further to select certain subset types as mentioned above.