How to download gc5Base file for hg38?

Question

[pranav5516]

Hi,

I would like to download GC percent data for hg38 for different window sizes, particularly 5bp. I can download this file from UCSC for hg19 but not for hg38.

Does anyone know a way? Thank you in advance for any help.

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Pranav

[pranav5516]

Yes I know, but with this option, the output file can only have 100,000 lines. I am interested in the whole genome. The same page says that 'the entire dataset may be available on downloads page'. But this page has gc%data only for hg19.

May be this file is not available at all for hg38 yet?

Answer 1

[PoGibas]

You can download "GC Percent" simply trough UCSC table browser. Select assembly ("hg38") and group ("Mapping and Sequencing").

Answer 2

[Sukhi Singh]

Just for the knowledgesake! GRCh37/38(NCBI) vs hg19/hg38(UCSC)

This is a direct FTP link to the required file: http://hgdownload.cse.ucsc.edu/gbdb/hg38/bbi/gc5BaseBw/gc5Base.bw

[Stephanie G.]

Thanks for that direct FTP link...

I am looking for the equivalent of http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gc5Base.txt.gz but in hg38. Any idea how can I convert this .bw (bigwig?) format into an identical format to the above link?

(Trying to perform CNV calling using pennCNV but with the hg38 genomebuild.)