CpG islands for ARS-UCD1.2 Bos taurus genome?

Question

[dango147]

Hi everyone,

I'm struggling to find CpG island annotations for the ARS-UCD1.2 bovine genome, any BED or similar file will do. I can see the tracks on the Genome Data Viewer (ncbi), but no way to download them. Oh, I've checked all the files available on the FTP sites but none of them had the information I need. Can somebody give me a hand to download those tracks?

Thanks!

Answer 1

[vkkodali_ncbi]

Please consider writing to the NCBI helpdesk with the question.

One way to generate your own CpG island data is to run the program cpg_lh from UCSC Kent tools on FASTA files that you can download from RefSeq FTP path. From the help text, here's how you can generate a bed formatted file:

cpglh fastaInput.fa \
 | awk '{$2 = $2 - 1; width = $3 - $2;
   printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n",
    $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \
     | sort -k1,1 -k2,2n > output.bed

[dango147]

Thanks vkkodali, that was helpful. I'll also write to the helpdesk

Answer 2

[vkkodali_ncbi]

NCBI Genome Data Viewer can now export CpG islands data (as well as other features such as repeats) in BED format; see changelog here. Simply go to GDV, enable the track and use the 'Download' button to download data.