can anybody tell me what all format do ucsc accepts? any guidance is appreciable
On Wed, Feb 3, 2010 at 2:21 PM, <[email protected]> wrote: > Send Genome mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.soe.ucsc.edu/mailman/listinfo/genome > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Genome digest..." > > > Today's Topics: > > 1. Bigbed doesn't show color (Carone, Benjamin) > 2. Re: FAQ pages have no extension (Ann Zweig) > 3. Re: FAQ pages have no extension (Wes Barris) > 4. Re: FAQ pages have no extension (Wes Barris) > 5. Re: How to dwonload genbank data 'genbank.168.0' ? (WANG Wuqi) > 6. Re: trying to get information in a particular format > (Jennifer Jackson) > 7. gene symbol and locus tag (Yuan Jian) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2010 13:13:32 -0500 > From: "Carone, Benjamin" <[email protected]> > Subject: [Genome] Bigbed doesn't show color > To: [email protected] > Message-ID: > < > e973d69eb7ff504382ac441f5df1e2722a3...@edunivmail06.ad.umassmed.edu> > Content-Type: text/plain; charset=iso-8859-1 > > Sorry, I figured out my problem, please disregard my previous email. > > Ben > > > ------------------------------ > > Message: 2 > Date: Tue, 02 Feb 2010 13:25:31 -0800 > From: Ann Zweig <[email protected]> > Subject: Re: [Genome] FAQ pages have no extension > To: Wes Barris <[email protected]> > Cc: Genome List <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello Wes, > > Thanks for pointing out this shortcoming. We have edited this page and > added > the .html extensions to the links. You can get the new file from CVS now, > or > wait until it's available for rsync: > > http://genome.ucsc.edu/admin/mirror.html#step2 > > > Regards, > > ---------- > Ann Zweig > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > Wes Barris wrote: > > The following page: > > > > http://genome.ucsc.edu/FAQ/ > > > > contains links to FAQ pages, however, the links do not contain > > any (.html) extension. What httpd configuration option is being > > used to serve these .html pages when the URL does not include the > > file extension? > > > > The reason I am asking is because our UCSC mirror is not serving > > these pages because of the missing file extensions in the links. > > > ------------------------------ > > Message: 3 > Date: Wed, 3 Feb 2010 08:45:46 +1000 > From: Wes Barris <[email protected]> > Subject: Re: [Genome] FAQ pages have no extension > To: Galt Barber <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > > Galt Barber wrote: > > I believe it is a very common httpd setting. > > It is going to loko for something like "index.html" > > if there is only a path without a filename, > > i.e. it ends in a slash. > > Perhaps I did not explain the issue well enough. I was not refering > to a URL ending in a directory (in which case a file like "index.html" > is served). I was referring to URLs that end in the basename of an > html page (without the .html extension). In any case, Ann Zweig > has modified the offending links. We should pick them up at the > next rsync. > > > --------- > > > > # DirectoryIndex: sets the file that Apache will serve if a directory > > # is requested. > > # > > # The index.html.var file (a type-map) is used to deliver content- > > # negotiated documents. The MultiViews Option can be used for the > > # same purpose, but it is much slower. > > # > > DirectoryIndex index.html index.html.var > > > > ---------- > > > > These is indeed an index.html under > > htdocs/FAQ > > > > -Galt > > > > Wes Barris wrote: > >> The following page: > >> > >> http://genome.ucsc.edu/FAQ/ > >> > >> contains links to FAQ pages, however, the links do not contain > >> any (.html) extension. What httpd configuration option is being > >> used to serve these .html pages when the URL does not include the > >> file extension? > >> > >> The reason I am asking is because our UCSC mirror is not serving > >> these pages because of the missing file extensions in the links. > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > -- > Wes Barris <[email protected]> > > > ------------------------------ > > Message: 4 > Date: Wed, 3 Feb 2010 08:46:54 +1000 > From: Wes Barris <[email protected]> > Subject: Re: [Genome] FAQ pages have no extension > To: Ann Zweig <[email protected]> > Cc: Genome List <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > > Ann Zweig wrote: > > Hello Wes, > > > > Thanks for pointing out this shortcoming. We have edited this page and > added > > the .html extensions to the links. You can get the new file from CVS > now, or > > wait until it's available for rsync: > > Thanks Ann. We should get them at the next rsync. > > > http://genome.ucsc.edu/admin/mirror.html#step2 > > > > > > Regards, > > > > ---------- > > Ann Zweig > > UCSC Genome Bioinformatics Group > > http://genome.ucsc.edu > > > > > > > > Wes Barris wrote: > >> The following page: > >> > >> http://genome.ucsc.edu/FAQ/ > >> > >> contains links to FAQ pages, however, the links do not contain > >> any (.html) extension. What httpd configuration option is being > >> used to serve these .html pages when the URL does not include the > >> file extension? > >> > >> The reason I am asking is because our UCSC mirror is not serving > >> these pages because of the missing file extensions in the links. > > > -- > Wes Barris <[email protected]> > > > ------------------------------ > > Message: 5 > Date: Wed, 3 Feb 2010 10:29:18 +0800 > From: WANG Wuqi <[email protected]> > Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > To: "'Hiram Clawson'" <[email protected]> > Cc: WANG Wuqi <[email protected]>, "[email protected]" > <[email protected]> > Message-ID: > < > 5c2622f7d7c5f340a63c90d92dc919f0c40cb1d...@pwex01.gis.a-star.edu.sg> > Content-Type: text/plain; charset="us-ascii" > > Hi Hiram, > > Many thanks for your information. > > I will upgrade databse mm8 depending on goldenPath/mm8/database/ files, > because our MySQL still is version 4.1.22. > > Thanks & Regards > > Wuqi > > > -----Original Message----- > From: Hiram Clawson [mailto:[email protected]] > Sent: Friday, January 29, 2010 11:12 PM > To: WANG Wuqi > Cc: [email protected] > Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > > > Good Morning: > > The /mysql/mm8/ directory are the actual MySQL binary files used by the > mysql system itself. If your mysql system is running version 5 of MySQL you > can rsync these binary files directly into your MySQL data directories and > avoid the database loading step. > > The goldenPath/mm8/database/ files are text dumps of the MySQL tables. > When you transfer these text dumps you need to run MySQL load commands to > get this data into your MySQL database. > > It is your choice of how you would like to do this. The text dump files > are smaller in size to transfer but they take some time to load into the > database. The binary files are larger because they include the MySQL > indexing information that MySQL created when the tables are loaded. > > --Hiram > > ----- Original Message ----- > From: "WANG Wuqi" <[email protected]> > To: "Brooke Rhead" <[email protected]> > Cc: "WANG Wuqi" <[email protected]>, [email protected] > Sent: Friday, January 29, 2010 12:08:04 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > > Hi Brooke Rhead, > > Our databases update from '/mysql/mm8/' insteag of > '/goldenPath/mm8/database/'. > > What is different between '/mysql/mm8/' insteag of > '/goldenPath/mm8/database/' for mm8 ? > > Please give advice > > > Thanks & Regards > > Wuqi > > > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Friday, January 29, 2010 2:38 PM > To: WANG Wuqi > Cc: [email protected] > Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > > > Hi Wuqi, > > The 'genbank.168.0' file no longer exists here. To correct the error, > update the tables from: > > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/database/ > > Specifically, you need new versions of the following tables: > > all_est > all_mrna > author > ccdsGene > ccdsInfo > ccdsKgMap > cds > cell > chr10_est > chr10_intronEst > chr10_mrna > chr10_random_est > chr10_random_intronEst > chr10_random_mrna > chr11_est > chr11_intronEst > chr11_mrna > chr12_est > chr12_intronEst > chr12_mrna > chr13_est > chr13_intronEst > chr13_mrna > chr13_random_est > chr13_random_intronEst > chr13_random_mrna > chr14_est > chr14_intronEst > chr14_mrna > chr15_est > chr15_intronEst > chr15_mrna > chr15_random_est > chr15_random_intronEst > chr15_random_mrna > chr16_est > chr16_intronEst > chr16_mrna > chr17_est > chr17_intronEst > chr17_mrna > chr17_random_est > chr17_random_intronEst > chr17_random_mrna > chr18_est > chr18_intronEst > chr18_mrna > chr19_est > chr19_intronEst > chr19_mrna > chr1_est > chr1_intronEst > chr1_mrna > chr1_random_est > chr1_random_intronEst > chr1_random_mrna > chr2_est > chr2_intronEst > chr2_mrna > chr3_est > chr3_intronEst > chr3_mrna > chr4_est > chr4_intronEst > chr4_mrna > chr5_est > chr5_intronEst > chr5_mrna > chr5_random_est > chr5_random_intronEst > chr5_random_mrna > chr6_est > chr6_intronEst > chr6_mrna > chr7_est > chr7_intronEst > chr7_mrna > chr7_random_est > chr7_random_intronEst > chr7_random_mrna > chr8_est > chr8_intronEst > chr8_mrna > chr8_random_est > chr8_random_intronEst > chr8_random_mrna > chr9_est > chr9_intronEst > chr9_mrna > chr9_random_est > chr9_random_intronEst > chr9_random_mrna > chrM_est > chrM_intronEst > chrM_mrna > chrUn_random_est > chrUn_random_intronEst > chrUn_random_mrna > chrX_est > chrX_intronEst > chrX_mrna > chrX_random_est > chrX_random_intronEst > chrX_random_mrna > chrY_est > chrY_intronEst > chrY_mrna > chrY_random_est > chrY_random_intronEst > chrY_random_mrna > description > development > estOrientInfo > gbCdnaInfo > gbExtFile > gbLoaded > gbMiscDiff > gbSeq > gbStatus > gbWarn > geneName > imageClone > keyword > library > mgcFullMrna > mgcGenes > mrnaClone > mrnaOrientInfo > organism > productName > refFlat > refGene > refLink > refSeqAli > refSeqStatus > refSeqSummary > sex > source > tissue > xenoMrna > xenoRefFlat > xenoRefGene > xenoRefSeqAli > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > WANG Wuqi wrote on 1/28/10 10:25 PM: > > Hi Brooke Rhead, > > > > When our users browse the tracks of mm8 to encounter problems, I find > > that the directory 'genbank.168.0' is empty. This may be rsync > > unsuccessful at that time. > > > > We have from 'genbank.162.0' to 'genbank.174.0', only missing > > 'genbank.168.0', If we can download this data, this will solve users' > > problems. > > > > Thanks & Regards > > > > Wuqi > > > > > > -----Original Message----- > > From: Brooke Rhead [mailto:[email protected]] > > Sent: Friday, January 29, 2010 11:46 AM > > To: WANG Wuqi > > Cc: [email protected] > > Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > > > > > > Hi Wuqi, > > > > You are correct: we only keep the most current genbank files. GenBank > > data files and many tables (such as gbLoaded, gbStatus, refGene, etc.) > > are updated frequently. Both the files AND the tables need to be > > up-to-date in order for the Genome Browser to work properly. It > > sounds like you need to update your tables so that they work with the > > latest > > (genbank.175.0) data files. > > > > Is there some reason you specifically need the 'genbank.168.0' version > > of the data files? > > > > -- > > Brooke Rhead > > UCSC Genome Bioinformatics Group > > > > > > On 01/28/10 19:00, WANG Wuqi wrote: > >> Hi Brooke Rhead, > >> > >> Thanks for your email. > >> > >> In fact, there is NOT 'genbank.168.0' in ftp server > >> ftp://hgdownload.cse.ucsc.edu/. > >> > >> Currently, only FTP directory has the following data, > >> > >> FTP directory /gbdb/genbank/data/processed/ at > >> hgdownload.cse.ucsc.edu To view this FTP site in Windows Explorer, > >> click Page, and then click Open FTP Site in Windows Explorer. > >> --------------------------------------------------------------------- > >> ----------- > >> Up to higher level directory > >> > >> 01/12/2010 06:33PM Directory . > >> 07/20/2008 12:00AM Directory .. > >> 01/24/2010 09:20AM Directory genbank.175.0 > >> 01/24/2010 09:20AM Directory refseq.38 > >> --------------------------------------------------------------------- > >> - > >> ---------- > >> > >> Here, does not have 'genbank.168.0' we wanted, so we can not rsync. > >> > >> Could you put this data temporarily to ftp server for our download. > >> > >> > >> Thanks & Regards > >> > >> Wuqi > >> > >> > >> > >> > >> -----Original Message----- > >> From: Brooke Rhead [mailto:[email protected]] > >> Sent: Friday, January 29, 2010 2:35 AM > >> To: WANG Wuqi > >> Cc: 'Hiram Clawson'; [email protected] > >> Subject: Re: [Genome] How to dwonload genbank data 'genbank.168.0' ? > >> > >> > >> Hello Wuqi, > >> > >> The genbank data and the genbank tables need to be kept in sync. You > >> may need to update either the files or the tables. Here is a > >> previously-answered question on the topic: > >> > >> https://lists.soe.ucsc.edu/pipermail/genome-mirror/2009-February/0011 > >> 6 > >> 2.html > >> > >> -- > >> Brooke Rhead > >> UCSC Genome Bioinformatics Group > >> > >> > >> > >> WANG Wuqi wrote on 1/27/10 10:15 PM: > >>> Hi Hiram, > >>> > >>> Our ucsc genome mirror side genbank data 'genbank.168.0' is missing, > >>> but in ftp://hgdownload.cse.ucsc.edu/, there is not such available > >>> data for download. > >>> > >>> Please give advice > >>> > >>> > >>> Thanks & regards > >>> > >>> Wuqi > >>> > >>> _______________________________________________ > >>> Genome maillist - [email protected] > >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > ------------------------------ > > Message: 6 > Date: Wed, 3 Feb 2010 00:15:14 -0800 (PST) > From: Jennifer Jackson <[email protected]> > Subject: Re: [Genome] trying to get information in a particular format > To: Carmen Iwaszczcenko <[email protected]> > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=utf-8 > > Hello Carmen, > > This exact format cannot be exported from the Table browser, > but a format that has the data per-feature (such as exon) would > be GTF. From there, the data could be transformed using your > own tools (perhaps even Excel) or in Galaxy (use "send output > to Galaxy). The section "Text Manipulation" would be a good place > to start. You could also contact their help list if you have questions. > > FAQ for GTF format: > http://genome.ucsc.edu/FAQ/FAQformat.html#format3 > http://genome.ucsc.edu/FAQ/FAQformat.html#format4 > > Table browser location & help: > http://genome.ucsc.edu/cgi-bin/hgTables > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html > > General path would be to: > 1) go to Table browser and navigate to the gene's track > 2) enter the gene's name/identifier > 3) select output format as GTF and either download or > send to Galaxy > > We apologize for the delay in our response, > Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > Subject: trying to get information in a particular format > Sent By > "Carmen Iwaszczcenko" <[email protected]> On: February > 1, 2010 11:13 AM > To: [email protected] > > Hello: > > I need the information to come out for a searched gene in this format: > > Exon Chromosome Start End (coordinate positions for the last 2). > > > > It needs to be text file (tab delimited) at the end, too. > > > > Is there a fast way to do this? > > > > Thanks, > > > > Carmen N. Iwaszczenko, BS > > Test Development Technologist > > PreventionGenetics LLC > > 3700 Downwind Drive > > Marshfield, WI 54449 > > PH: (715) 387-0484 x 106 > > FAX: (715) 384-3661 > > [email protected] > > > > The information contained in this e-mail message (including attachments) is > intended only for the personal and confidential use of the recipient(s) > named above. If the reader of this message is not the intended recipient or > an agent responsible for delivering it to the intended recipient, you are > hereby notified that you have received this document in error and that any > review, dissemination, distribution, or copying of this message is strictly > prohibited. If you have received this communication in error, please notify > us immediately by e-mail, and delete the original message. > > > > > ------------------------------ > > Message: 7 > Date: Tue, 2 Feb 2010 21:59:53 -0800 (PST) > From: Yuan Jian <[email protected]> > Subject: [Genome] gene symbol and locus tag > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=iso-8859-1 > > Hello, > ? > what table should I download from to find gene symbol by given Locus tag? > ? > I am using yeast Saccharomyces cerevisiae > for example: > Locus Tag???? gene Symbol > YKL113C????? RAD27 > .... > ? > thanks > ? > YU > > > > > __________________________________________________________________________________ > Yahoo!7: Catch-up on your favourite Channel 7 TV shows easily, legally, and > for free at PLUS7. www.tv.yahoo.com.au/plus7 > > ------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > End of Genome Digest, Vol 85, Issue 6 > ************************************* > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
