Chromosome Name Converter

Different files using different chromosome naming systems for the same genome build presents a challenge during analysis. This tool is provided as a converter between chromosome naming systems for tab-delimited file formats such as BED and GFF.

Arabic ↔ Roman
chr1 ↔ chrI
chr2 ↔ chrII
chr3 ↔ chrIII
...
chr16 ↔ chrXVI

More specifically, the sacCer3 genome build uses an arabic numeral naming system (chr1 through chr16) or a roman numeral naming system (chrI through chrXVI). This script serves as a converter between these naming systems and includes options around the mitochondrial and 2-micron naming features.

chrM ↔ chrmt

Also, a mitochondiral chromosome name conversion is also included with the selection of a checkbox option.

Command Line Interface

Convert BED Chr Names

Usage:

java -jar ScriptManager.jar file-utilities convert-bed-genome [-ahmV] [-o=<output>] <coordFile>

Description:

Convert BED coordinate files between the standard SGD roman numeral chromosome names to the legacy SacCer3_cegr arabic numeral chromosome names.

Convert GFF Chr Names

Usage:

java -jar ScriptManager.jar file-utilities convert-gff-genome [-ahmV] [-o=<output>] <coordFile>

Description:

Convert GFF coordinate files between the standard SGD roman numeral chromosome names to the legacy SacCer3_cegr arabic numeral chromosome names.

Positional Input

Expects a single BED file or GFF file for input.

Output Options

Option	Description
-o, --output=<output>	specify output directory (name will be same as original with .bed ext)

Conversion Options

Option	Description
-a, --to-arabic	switch converter to output arabic numeral chromsome names (default outputs roman numeral chrnames)
-m, --chrmt	converter will map "chrM" --> "chrmt" (default with no flag is "chrmt" --> "chrM")