Questions › Category: BIOSTAR › How to do the exercise from the book with Chr22 and hg38 but with hg37
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alvaradohernab2@nih.gov asked 6 months ago

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 Answers
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stonelakeak@nih.gov Staff answered 6 months ago

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