The chrom alias mechanism functions automatically in the genome browser for custom track data and track hub data. It will convert chromosome names from alternate naming schemes to the names used in the assembly in the genome browser.
The first line of the chromAlias.txt file begins with the pound symbol # followed by a blank space. Subsequent words, separated by a tab character, on this first line are the identification of the source authority for names in that column of the file. The first column set of names are the names of sequences used in the genome browser sequence. Subsequent columns are alternate naming schemes.
The lines following that first column header title line are columns of sequence names separated by a tab character. For the case of no equivalent name in that name space, the column is empty, there will be two adjacent tab characters.
# ucsc assembly genbank ncbi refseq chr1 1 CM000663.2 1 NC_000001.11 chr10 10 CM000672.2 10 NC_000010.11 chrX X CM000685.2 X NC_000023.11 chrM MT J01415.2 MT NC_012920.1
In this example the columns are:
- ucsc - UCSC style chrN names
- assembly - names from NCBI file assembly_report.txt
- genbank - INSDC names
- ncbi - from chr2acc file in assembly_structure/ hierarchy
- refseq - names from RefSeq annotations
To use the chromAlias.txt file in a track hub, in the genome stanza, specify
which is a relative path reference from this hub.txt file.
genome GCF_000001405.39 taxId 9606 groups groups.txt description human twoBitPath GCF_000001405.39.2bit twoBitBptUrl GCF_000001405.39.2bit.bpt chromSizes GCF_000001405.39.chrom.sizes.txt chromAlias GCF_000001405.39.chromAlias.txt organism human defaultPos chr1:82985474-82995474 scientificName Homo sapiens htmlPath html/GCF_000001405.39_GRCh38.p13.description.html