How to get the genomic coordinates of a transcripts in EntrezDirect ?
I have learnt how to get the coding coordinates of a transcripts here Easy way to compare the co-ordenates between RefSeq transcripts. I was wondering how to get the genomics coordinates
1 answer
$ esearch -db nuccore -query NM_002734.5 | elink -target gene | esummary | xtract -pattern DocumentSummary -element AssemblyAccVer,ChrAccVer,ChrStart,ChrStop
GCF_000001405.40 GCF_009914755.1 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.39 GCF_000001405.38 GCF_000001405.25 GCF_000001405.25 GCF_000001405.25 GCF_000002125.1 GCF_000306695.2 NC_000017.11 NC_000017.11 NC_060941.1 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.11 NC_000017.10 NC_000017.10 NC_000017.10 AC_000149.1 NC_018928.2 68413622 68413622 68413622 69290145 68413622 68413622 68413622 68413622 68413622 68413622 68413622 68413622 68413622 68413622 68413622 66409763 66409763 66507920 61893654 66572676 68551315 68551315 69428168 68551315 68551315 68551315 68551315 68551315 68551315 68551315 68551315 68551315 68551315 68551315 66547456 66547456 66547456 61933190 66612183
Above is bit messy but this would be concise (only works for the latest accession).
$ esearch -db nuccore -query NM_002734.5 | elink -target gene | esummary | xtract -pattern GenomicInfo -element ChrAccVer,ChrStart,ChrStop
NC_000017.11 68413622 68551315
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Download the suitable GTF file, it is all annotated in there. Since splicing comes into play there won't be a single interval unless it is an intronless gene.
Thanks for your help. I have found this https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/
The file hg19.ncbiRefSeq.gtf.gz shown the transcripts but only the last version. I want to search across different versions. I cannot find a file with old versions
Hg19 is also known as GRCh37, data from past Hg19 versions, aka releases, are available at http://ftp.ensembl.org/pub/grch37/