question about FASTA file extracted from RSAT
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3.8 years ago
kanwarjag ★ 1.1k
>Homo_sapiens-ENSG00000186115-CYP4F2-ENST00000011989    ENSG00000186115-ENST00000011989; downstream from -2000 to -1; size: 2000; location: chromosome:GRCh38:19:1:58617616:1 15878301 15880300 R

I used RSAT tool extract FASTA file. I get the header as above I pretty much understand most of the header information, however I am not sure what is referring to 1:58617616.

Thanks

ChIP-Seq • 698 views
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3.8 years ago

it's the size of the chr19

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg38 -e 'select chrom,size from chromInfo where chrom="chr19"'
+-------+----------+
| chrom | size     |
+-------+----------+
| chr19 | 58617616 |
+-------+----------+
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$ wget -O- -q https://genome.ucsc.edu/goldenpath/help/hg38.chrom.sizes | grep -w chr19
chr19   58617616
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