[Genome] short mm8 chr1 and 2?

[Rachel Harte]

Hello Ben,

It may be that if you are using Windows and http then the files are not
being completely downloaded. Try using wget and ftp instead e.g. for chr1:
wget
'ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/mm8/chromosomes/chr1.fa.gz'
-O chr1.fa.gz

--18:54:24--
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/mm8/chromosomes/chr1.fa.gz
           => `chr1.fa.gz'
Resolving hgdownload.cse.ucsc.edu... 128.114.119.140
Connecting to hgdownload.cse.ucsc.edu|128.114.119.140|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD /apache/htdocs/goldenPath/mm8/chromosomes
... done.
==> PASV ... done.    ==> RETR chr1.fa.gz ... done.
Length: 62,819,741 (60M) (unauthoritative)

100%[====================================>] 62,819,741    13.69M/s    ETA
00:00

18:54:28 (14.16 MB/s) - `chr1.fa.gz' saved [62819741]

then
>sum chr1.fa.gz
52962 61348

For chr2:
--18:58:03--
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/mm8/chromosomes/chr2.fa.gz
           => `chr2.fa.gz'
Resolving hgdownload.cse.ucsc.edu... 128.114.119.140
Connecting to hgdownload.cse.ucsc.edu|128.114.119.140|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD /apache/htdocs/goldenPath/mm8/chromosomes
... done.
==> PASV ... done.    ==> RETR chr2.fa.gz ... done.
Length: 58,461,619 (56M) (unauthoritative)

100%[====================================>] 58,461,619    14.54M/s    ETA
00:00

18:58:07 (14.51 MB/s) - `chr2.fa.gz' saved [58461619]

then
> sum chr2.fa.gz
24876 57092

If your result does not look like the output above then the file is not
being downloaded completely.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Mon, 30 Apr 2007, Ben Gantner wrote:

> Hi there:
>
> Sorry for the bother but I've tried repeatedly to download
> the mm8 release of the mouse genome from your site. I'm
> downloading gzipped files from the following page:
> http://hgdownload.cse.ucsc.edu/goldenPath/mm8/chromosomes/
>
> When I decompress the files I count the total sequence length
> per chromosome (minus headers) and I get back the correct
> lengths for most of the chromosomes as described on your
> site:
> http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=86540626&chromInfoPage=
>
> However, chr1 and chr2 show up short, and I'm missing a
> significant amount of sequence:
> chr1 get : 115212860, expect : 197,069,962
> chr2 get : 102088474, expect : 181,976,762
>
> I've looked through the site FAQ and can't find anything
> about this, any suggestions/ideas??
>
> Thanks so much,
> Ben
> _________________________
> Ben Gantner
> University of Chicago
> Singh Lab, CIS Rm W519
> 929 East 57th Street
> Chicago, IL  60637
> (Ph) 773.702.2912
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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>