Chromosomes can be named freely, but the names need to be the same for all data that are analyzed together.

So if you e.g. would like to create a heatmap of ChIP-seq signal at enhancers, but the enhancer Regionset use a different naming than the Datasets, then EaSeq has a wizard that will check if the chromosome names of imported data correspond to those found in already imported data, and if they do not correspond, it will help you renaming the chromosomes.

Although EaSeq will not complain if chromosomes are named John, Paul, George, and Ringo, it will be more challenging to relate the data to other data, so the easiest would be to stick to the most commonly used names for that particular organism.

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