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.

File inputs

There is a separate tool for BED and GFF processing (make sure to use appropriate extensions).

Conversion options

To Arabic or To Roman

The chromosome names can be converted either from Arabic to Roman (chr3 → chrIII) or from Roman to Arabic (chrIII → chr3).

Use "chrmt" instead of default "chrM"

Since some genome builds use "chrmt" instead of "chrM", this checkbox gives the user the option to specify the mitochondrial chromsome naming format.

Output options (BED/GFF)

The first tab-delimited token is a string corresponding to a chromosome name and mapped to its appropriate arabic or roman numeral equivalent according to the selected conversion option. The output filepath is derived from the input filename with its extension stripped (.bed or .gff) and replaced with either a _toRoman.bed or _toArabic.bed suffix accordingly (.gff suffix if using GFF tool).

Output GZip

Toggling this allows the user to write output to a compressed file format using a general compression (gzip) which has the added advantage of speeding up the execution time by shrinking the I/O load (esp for large output). The .gz extension will be appended as appropriate.

Command Line Interface

Convert BED Chr Names

Usage:

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

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")