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

[Galt Barber]

It may be necessary to process one chromosome at a time to reduce the 
memory requirements.  Using -stepSize=5 increases the sensitivity,
but it also increases RAM usage. You can usually get adequate results
without it, that might be enough RAM savings. I can process the
human genome on a 1GB machine, even with -stepSize=5, if I
run BLAT one chromosome at a time.  It takes several GB of RAM
to blat the entire human genome at once.

(See the BLAT FAQ)


A note on filtering output:
Use either the pslReps or pslCDnaFilter program available in the Genome 
Browser source code to filter for the size, score, coverage, or quality 
desired. For information on obtaining the source code, see our FAQ on 
source code licensing and downloads.

-Galt


On Tue, 20 May 2008, Li, Jianying (NIH/NIEHS) [C] wrote:

> 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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>
> _______________________________________________
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