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How to do the exercise from the book with Chr22 and hg38 but with hg37
I typed this command
$ curl https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz | gunzip -c > ~/refs/hg37/chr22.fa
But It just show up the next
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
1 Answer:
Hello, Do you mean GRCh37(hg19)? The URL is correct, I believe it is the download folder that is the problem. Try this: Create directories for your refs and GRCh37/hg19 data and change to that directory mkdir refs cd refs mkdir GRCh37 cd GRCh37 Now try the command line like this: curl https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz | gunzip -c > chr22.fa Another way: You can only download into ~/refs/hg37 dir if you have created it first. To create it: mkdir -p ~/refs/hg37 Then you can use the command you were trying before curl https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz | gunzip -c > ~/refs/hg37/chr22.fa Let me know if that works for you. The command line you were trying might not have worked if you had not created the dir ~/refs/hg37 yet
Answered on April 24th, 2020 by amy.stonelake@nih.gov