dpryan79 / chromosomemappings Goto Github PK

Hi, thanks for sharing these tables. I'm working with Ensembl accessions and Genome Reference Consortium issue mapping, and the GenBank (nuccore) accession is the only way I can find to map the issue title to the chromosome/contig name.

This isn't as straightforward as it first looks for some patches (e.g. issue HG-1703 maps to contig name HG237_PATCH (via GenBank ID: KE332506.1, matched through your table).

I'd really like to add these mappings to the tables of issues I've made from processing the GRC XML but I can't find the source you've used.

Could you please suggest where/how I could reproduce the mappings in the Ensembl ⇒ Gencode tables?

:)

The GRCh38_UCSC2ensembl.txt file is missing contig mapping from the hg38 UCSC side. In using this file to remap UCSC contigs to Ensembl the map fails because of missing contigs.

For example, chr10_KN196480v1_fix, chr10_KQ090021v1_fix, chr11_KN196481v1_fix, etc. are all within the file being remapped, but these contigs are not in GRCh38_UCSC2ensembl.txt.

I am unaware of other files that may be missing updated contigs, but there may be a few.

Could you update the GRCh38_UCSC2ensembl.txt file, and potentially other files that are missing updated contigs?

Mouse got an update today and human a couple days ago, the "recent" patches/fixes need to get included. I should also check for updates to zebra fish and fruit fly. If someone else would like to do one of these then feel free :)

• GRCm38
• GRCh38

I should probably start doing this every six months or so.

Hi Ryan,

Thanks for this handy tool!

I've tried to use it, and the following error message pops up.
Is it something to do with the settings of my computer?

Unrecognized VM option 'AggressiveOpts'
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

Thanks!
Chiefcat

Thanks for compiling these tables. Could you comment on their sources?

Namely, the mappings between patches in Ensembl and NCBI are wrong, since Ensembl N-pads contigs while NCBI doesn't. This should be checked and clarified in the repo.

What is the license for this directory? Would it be possible to add the license to it? There's a tool in development in which we would like to use these files as a part of.

Thanks in advance!

I've created ucsc<->ensembl mappings for the galGal4 chicken genome, but I don't know how to upload them due to permissions. My github user name is iljungr.