a question in UCSC Executable:netClass

[王明山]

Dear UCSC Genome Bioinformatics Group memebers,

       I‘m a graduate student  doing research in bioinformatics.Recently,I want to get genome alignment *.maf files using genome human (hg19) and bushbaby(otoGar3) from UCSC by processes described in http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_ howto,I have done step 1(alighment with Blastz) and step 2(Chaining),but in step 3 (Netting),I have done chainNet and get noClass.net format  alighment file successfully ,but something was wrong when  I use executable netClass  "netClass -noAr noClass.net tDb qDb noClass.net " to add classification information,I don't  know what tDb qDb files are and how I can get it.From command: 

 "./netClass"
netClass - Add classification info to net
usage:
   netClass [options] in.net tDb qDb out.net
       tDb - database to fetch target repeat masker table information
       qDb - database to fetch query repeat masker table information

I think tDb  and qDb files may be repeat masker files from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz(hg19_rmsk.txt) and http://hgdownload.soe.ucsc.edu/goldenPath/otoGar3/database/rmsk.txt.gz(otoGar3_rmsk.txt) ,is that right? So run the command

" ./netClass noClass.net hg19_rmsk.txt otoGar3_rmsk.txt Class.net",but get error :

Couldn't connect to database hg19_rmsk.txt on localhost as root.
Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)

It troubles me many days, Can you tell me how to do with netClass?Thank you very much!

Best wishes!

Wang Mingshan

 

[Brooke Rhead]

Hello Wang Mingshan,

The tDb and qDb arguments to netClass do not specify files, but
databases. netClass expects MySQL databases to exist for the "from"
assembly and the "to" assembly, and for repeatmasker tables (named
"rmsk", but with the -qRepeats and -tRepeats options can be named
something else) to reside in each database. A lot of our tools assume
access to a database, and for assemblies that we host at UCSC, we have
instructions on how to set up an .hg.conf file in your home directory so
that can access databases on our public MySQL server:

http://genome.ucsc.edu/goldenPath/help/mysql.html

If you are aligning assemblies that are not hosted by UCSC, you could
set up your own MySQL server and put information for accessing it into a
.hg.conf file in your home directory.

One of our engineers suggests an alternative to all of the above: skip
this step of the alignment process described in genomewiki, and move
noClass.net to the file you want as output. There is no downstream
dependency in the pipeline for the class information to be in the *.net
file (except for in the Genome Browser), so you could just do something
like this:

mv noClass.net $tdb.$qdb.net

and then you won't need a database at all.

I hope this is helpful. If you have other questions about the UCSC
Genome Browser, please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 2/21/13 4:05 AM, 王明山 wrote:
>
> Dear UCSC Genome Bioinformatics Group memebers,
>

> I‘m a graduate student doing research in bioinformatics.Recently,I want

> to get genome alignment *.maf files using genome human (hg19) and
> bushbaby(otoGar3) from UCSC by processes described in

> _http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_ howto_

> <http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto>,I
> have done step 1(alighment with Blastz) and step 2(Chaining),but in step
> 3 (Netting),I have done chainNet and get noClass.net format alighment
> file successfully ,but something was wrong when I use executable

> netClass *"netClass -noAr noClass.net tDb qDb noClass.net "* to add
> classification information,I don't know *what tDb qDb files are and how
> I can get it*.From command:
>
> "*./netClass"

> netClass - Add classification info to net
> usage:
> netClass [options] in.net tDb qDb out.net
> tDb - database to fetch target repeat masker table information

> qDb - database to fetch query repeat masker table information*
>
> *I think tDb and qDb files may be repeat masker files from
> *_http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz_(hg19_rmsk.txt
> <http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz(hg19_rmsk.txt>)
> and
> _http://hgdownload.soe.ucsc.edu/goldenPath/otoGar3/database/__rmsk.txt.gz_(otoGar3_rmsk.txt)
> ,*is that right? *So
> <http://hgdownload.soe.ucsc.edu/goldenPath/otoGar3/database/rmsk.txt.gz(otoGar3_rmsk.txt)%20,is%20that%20right?
> So>run the command
>
> *" ./netClass noClass.net hg19_rmsk.txt otoGar3_rmsk.txt Class.net",but
> get error :*
>
> *Couldn't connect to database hg19_rmsk.txt on localhost as root.

> Can't connect to local MySQL server through socket

> '/var/lib/mysql/mysql.sock' (2)*

>
> It troubles me many days, Can you tell me how to do with netClass?Thank
> you very much!
>
> Best wishes!
>
> Wang Mingshan
>

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