How would one map (say) the Refseq genomic region NG_017013.2 to a location on GRCh37?
I've looked on its NCBI info page with no luck, and the UCSC Table Browser doesn't appear to have a table of NG_ region mappings, unless I'm mistaken.
Thanks in advance for looking!
Try this file: ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/GCF_000001405.25_refseqgene_alignments.gff3
There is a 'Download' link on the RefSeqGene page (http://www.ncbi.nlm.nih.gov/refseq/rsg/)- this file (and others) will do what you need.
This has bugged me for a long time! Thanks @nmb for asking and @deanna.church for answering.
Now that you have the GFF3 file on disk, you can
$ cat GCF_000001405.25_refseqgene_alignments.gff3 | grep NG_017013.2 | cut -f1 -f4 -f5
NC_000017.10 7563097 7595868
to get the chromosome, start and end positions of that RefSeqGene.
Great! glad that was helpful.
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deanna.church
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