Question: question about FASTA file extracted from RSAT
0
gravatar for kanwarjag
2.7 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:
>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 • 590 views
ADD COMMENTlink modified 2.7 years ago by Pierre Lindenbaum129k • written 2.7 years ago by kanwarjag1.0k
0
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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 |
+-------+----------+
ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum129k
$ wget -O- -q https://genome.ucsc.edu/goldenpath/help/hg38.chrom.sizes | grep -w chr19
chr19   58617616
ADD REPLYlink written 2.7 years ago by cpad011213k
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