Mapping Refseq Ng_ Regions To Chromosome Position

Question

[nmb]

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!

Answer 1

[deanna.church]

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.

Answer 2

[Hugues]

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.

[deanna.church]

Great! glad that was helpful.