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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Refine rat and worm genomes #233

Closed eweitz closed 4 years ago

eweitz commented 4 years ago

This refines chromosome data for Norway rat (Rattus norvegicus) and nematode worm (Caenorhabditis elegans).

Worm (C. elegans) genome data has been inlined, speeding up ideogram creation.

Rat genome data has been improved as follows:

Notably, rat chromosome Y uses lengths from the non-assembled molecule -- because the usual assembled length is drastically smaller than the actual rat chrY. General centromere positions derive from literature, especially Hamta et al. (2006). "Chromosome ideograms of the laboratory rat (Rattus norvegicus) based on high-resolution banding, and anchoring of the cytogenetic map to the DNA sequence by FISH in sample chromosomes." Cytogenetic and Genome Research, 115(2), 158–168. doi:10.1159/000095237.

A visual summary of the rendering improvements for R. norvegicus is below.

Rat genome before

rat_genome_before_improvements_ideogram

Rat genome after

Banded, with refined centromeres and chromosome MT:

rat_genome_after_improvements_ideogram

Unbanded:

rat_genome_unbanded_ideogram
coveralls commented 4 years ago

Coverage Status

Coverage decreased (-0.07%) to 89.364% when pulling 93f3b534fb6d32e06f76248cceb7a002e68356d1 on refine-rat-and-worm-genomes into c4a2d6b9e6b36609a2e31cba21355759b7bf5a0d on master.