Question: How to download gc5Base file for hg38?
0
gravatar for pranav5516
5.0 years ago by
pranav55160
Germany
pranav55160 wrote:

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.

--

Pranav

genome • 2.2k views
ADD COMMENTlink modified 12 days ago by Biostar ♦♦ 20 • written 5.0 years ago by pranav55160

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?

 

ADD REPLYlink written 5.0 years ago by pranav55160
2
gravatar for PoGibas
5.0 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

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

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by PoGibas4.8k
1
gravatar for Sukhdeep Singh
4.3 years ago by
Sukhdeep Singh9.9k
Netherlands
Sukhdeep Singh9.9k wrote:

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

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Sukhdeep Singh9.9k

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.)

ADD REPLYlink written 21 months ago by Stephanie G.0
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