[Genome] chromTrf.tar.gz for mm9 contains symlinks but no data

[Li, Jianying (NIH/NIEHS) [C]]

Hi, Ann & all,

I am trying to do BLAT search on my local computer, basically BLAT NCBI
UniGene sequences against Rat Genome in order to get the chromosomal
coordinates. 

However, when I ran it, I got out of memory error. Could you please help
me with this, i.e. how much memory do I need to run such BLAT search?

Thanks.

Jianying Li

-----Original Message-----
From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
Sent: Wednesday, May 07, 2008 12:54 PM
To: Herve Pages
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] chromTrf.tar.gz for mm9 contains symlinks but no
data

Hello Herve,

	Sorry about the corrupt file -- thanks for bringing it to our 
attention.  We have replaced it with the correct file at the same
location.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Herve Pages wrote:
> Hi,
> 
> I've downloaded the chromTrf.tar.gz file (Tandem Repeats Finder
locations) for
> mm9 (the file is here:
http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/)
> but it contains symlinks only:
> 
>    hpages at lamb1:~/BSgenome_srcdata/UCSC/mm9/masks> tar ztvf
chromTrf.tar.gz
>    lrwxrwxrwx hiram/protein     0 2007-07-25 10:25:14
trfMaskChrom/chr1.bed -> ../trf/chr1.bed
>    lrwxrwxrwx hiram/protein     0 2007-07-25 10:25:14
trfMaskChrom/chr1_random.bed -> 
> ../trf/chr1_random.bed
>    lrwxrwxrwx hiram/protein     0 2007-07-25 10:25:14
trfMaskChrom/chr10.bed -> ../trf/chr10.bed
>    lrwxrwxrwx hiram/protein     0 2007-07-25 10:25:14
trfMaskChrom/chr11.bed -> ../trf/chr11.bed
>    lrwxrwxrwx hiram/protein     0 2007-07-25 10:25:14
trfMaskChrom/chr12.bed -> ../trf/chr12.bed
>    ...
>    etc...
> 
> so there seems to be nothing I can do with it.
> Where can I find the Tandem Repeats Finder locations for mm9?
> 
> Any help would be highly apreciated. Thanks!
> H.
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome

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