Hi Peter, This is Venu Valmeekam from Affymetrix. We create custom tracks of our probesets on the ucsc genome browser and provide links to them in Netaffx website (http://www.affymetrix.com/analysis/index.affx) probeset reports. You have to be registered to use the NetAffx website, but that should be fairly straightforward. Once you register you can run a query on any of the arrays that you are interested in and go to the detail report of one probeset and the report contains links to the ucsc genome browser, that will automatically load a custom track for you.
Please let me know which arrays you are interested in and I can provide more precise details on how to launch those custom tracks. Thanks, Venu Venu Valmeekam, Ph.D | Staff Bioinformatics Engineer II | Software Engineering AFFYMETRIX, INC. | 6550 Vallejo Street, Suite 100 | Emeryville, CA 94608 | Tel: 510-428-8554 | Fax: 510-428-8585 -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Tuesday, February 02, 2010 10:55 AM To: [email protected] Subject: Genome Digest, Vol 85, Issue 4 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. Re: HOW TO DOWNLOAD GENE REGULATORY NETWORK DATA. (Jennifer Jackson) 2. Re: Affymetrix probe sets (Jennifer Jackson) 3. FAQ pages have no extension (Wes Barris) 4. *.nib files in Scer2 7-way alignment (meritxell oliva) 5. Creating own MAF track (Tomas Vinar) 6. Looking for Annotation file (Pratap, Abhishek) 7. buffer overflow in ucsc genome browser (Matthew Bainbridge) 8. Re: buffer overflow in ucsc genome browser (Jennifer Jackson) 9. Re: Looking for Annotation file (Jennifer Jackson) ---------------------------------------------------------------------- Message: 1 Date: Mon, 1 Feb 2010 15:19:55 -0800 (PST) From: Jennifer Jackson <[email protected]> Subject: Re: [Genome] HOW TO DOWNLOAD GENE REGULATORY NETWORK DATA. To: sourav bhattacharya <[email protected]> Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Hello, For several of the reference genome assemblies, under the track group "Regulation", there are tracks that may be useful. Read the track descriptions to understand contents, methods, and data models ("view schema"). To download: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "sourav bhattacharya" <[email protected]> wrote: > From: "sourav bhattacharya" <[email protected]> > To: [email protected] > Sent: Saturday, January 30, 2010 10:53:54 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] HOW TO DOWNLOAD GENE REGULATORY NETWORK DATA. > > I am working on gene regulatory network.and i need some sample network > of > genetic regulation.from where i can get this... > > please give advice. > > thanks & regards. > > Sourav. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ Message: 2 Date: Mon, 1 Feb 2010 15:37:21 -0800 (PST) From: Jennifer Jackson <[email protected]> Subject: Re: [Genome] Affymetrix probe sets To: Peter Hevezi <[email protected]> Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Hello Peter, You are correct, the latest human assembly has not been fully populated with all of the tracks available in the prior assembly (nothing has been deleted, the tracks still exist in the prior assemblY). Over time, some of these will be moved to the new assembly and some will not. The idea of creating a Custom track is a good one. Extract the data from the prior assembly, use liftOver to convert the coordinates to the new assembly, and load in the new assembly. http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://hgdownload.cse.ucsc.edu/downloads.html -> scroll to Source Downloads/LiftOver tool Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Peter Hevezi" <[email protected]> wrote: > From: "Peter Hevezi" <[email protected]> > To: [email protected] > Sent: Monday, February 1, 2010 10:32:17 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Affymetrix probe sets > > Previous versions of the browser had annotation that mapped affymetrix > probe > set sequences on the genome. I found this feature extremely useful. > This > track seems to have been deleted in the recently released version. Is > there > a way of adding the annotation using the custom annotation tracks > feature? > > > > Thanks, > > > > Peter Hevezi > > University of California, Irvine > > > > [email protected] > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ Message: 3 Date: Tue, 2 Feb 2010 11:47:59 +1000 From: Wes Barris <[email protected]> Subject: [Genome] FAQ pages have no extension To: Genome List <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed 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 ------------------------------ Message: 4 Date: Tue, 2 Feb 2010 02:35:09 +0100 From: meritxell oliva <[email protected]> Subject: [Genome] *.nib files in Scer2 7-way alignment To: [email protected] Cc: Cedric Notredame <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 Dear UCSCers, I'm trying to reproduce the Scer2 7-way alignment, as in http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/sacCer2.txt . Before running blastz, genomes are usually faToNib-masked for repeats, like in the example based on ciona alignments: http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto In the yeast alignment, this step is missing. Am I right? If so, why? I mean, which should be the criteria to include/skip this step? . Even if *.nib files are not necessary to feed blastz, it seems that they are necessary to carry out the axtChain-chaining step. Is that right? . Although chain.csh is created for the chaining step, I don't see axtChain invoked anywhere in the pipeline. I can only observe that *.chain files are created somehow and then used to feed chainMergeSort. Could you please clarify how is the chaining step performed? Thanks in advance Meritxell Oliva PhD Student Comparative Bioinformatics Group Bioinformatics and Genomics Programme Centre de Regulacio Genomica (CRG) Dr. Aiguader, 88 08003 Barcelona Spain email: [email protected] . ------------------------------ Message: 5 Date: Tue, 2 Feb 2010 13:39:36 +0100 From: Tomas Vinar <[email protected]> Subject: [Genome] Creating own MAF track To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 Hello, I am trying to create a browser for new species in my local copy of the genome browser. I have created and succesfully loaded maf alignment tracks, and the displayed results look as expected. However, when I click on the maf track to display the actual alignment, the hgc starts allocating large amounts of memory (>3 GB) and does not return expected results (probably gets killed for using too many resources). Note that these are really small genomes I am working with (sequences of less than 30Kbp) and the maf alignment has about 1MB. Do you know any reason why this should be happening? Here is the definition of the track from trackDb.ra: track mafCandida shortLabel Multiz Align longLabel Multiz Alignments summary mafCandidaSummary spanList 1 maxHeightPixels 100:40:11 autoScale Off windowingFunction mean group compGeno color 0, 10, 100 altColor 0,90,10 type wigMaf 0.0 1.0 priority 100 visibility pack -- -------------------------------------------------------------------------- Tomas Vinar, Assistant Professor Department of Applied Informatics Faculty of Mathematics, Physics, and Informatics Comenius University, Bratislava E-mail: [email protected] Office: M163 Work Phone: +421-2-60295207 ------------------------------ Message: 6 Date: Tue, 2 Feb 2010 11:49:16 -0500 From: "Pratap, Abhishek" <[email protected]> Subject: [Genome] Looking for Annotation file To: "[email protected]" <[email protected]> Message-ID: <b58c34d85cf5a04fa38c2e9176f26dd101b3a...@issommail01.som.umaryland.edu> Content-Type: text/plain; charset="us-ascii" Hi Jennifer and All I am looking to get annotation info for the following genome. Saccharophagus_degradans_2-40 I see NCBI has info on it. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19331 I am not sure where to get hold of gene annotation. Thanks for your help! -Abhi ------------------------------ Message: 7 Date: Tue, 2 Feb 2010 08:06:59 -0600 From: Matthew Bainbridge <[email protected]> Subject: [Genome] buffer overflow in ucsc genome browser To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1 I get a buffer overflow in ucsc genome browser. I'm fairly certain its because my track name is over 128 characters. I'm happy enough to use a shorter track name but because of the buffer overflow, I can't modify or delete the existing track. The exact error (on delete) is: buffer overflow, size 128, format: %s_%s Thanks, M ------------------------------ Message: 8 Date: Tue, 2 Feb 2010 10:13:07 -0800 (PST) From: Jennifer Jackson <[email protected]> Subject: Re: [Genome] buffer overflow in ucsc genome browser To: Matthew Bainbridge <[email protected]> Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Hello Matthew, To double check - you are using Custom tracks at the UCSC Browser site http://genome.ucsc.edu/ ? Has this been added to the Sessions database? If you would send me the track name (directly, not to list) we can delete here. If this is in a Session, please send your user name, too. Meanwhile, the best advice is to just ignore it. Custom tracks are temporary anyway (48 hours). Thank you for the feedback, Jennie ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Matthew Bainbridge" <[email protected]> wrote: > From: "Matthew Bainbridge" <[email protected]> > To: [email protected] > Sent: Tuesday, February 2, 2010 6:06:59 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] buffer overflow in ucsc genome browser > > I get a buffer overflow in ucsc genome browser. I'm fairly certain > its because my track name is over 128 characters. > I'm happy enough to use a shorter track name but because of the > buffer overflow, I can't modify or delete the existing track. > > The exact error (on delete) is: > buffer overflow, size 128, format: %s_%s > > Thanks, > M > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ Message: 9 Date: Tue, 2 Feb 2010 10:54:29 -0800 (PST) From: Jennifer Jackson <[email protected]> Subject: Re: [Genome] Looking for Annotation file To: Abhishek Pratap <[email protected]> Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Hi Abhi, Use the UCSC Archaeal Genome Browser http://archaea.ucsc.edu/ Saccharophagus degradans 2-40 03/17/2006 (saccDegr_2_40) assembly There is a RefSeq track with about 4k entries. We hope this helps, Jennier ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Abhishek Pratap" <[email protected]> wrote: > From: "Abhishek Pratap" <[email protected]> > To: [email protected] > Sent: Tuesday, February 2, 2010 8:49:16 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Looking for Annotation file > > Hi Jennifer and All > > I am looking to get annotation info for the following genome. > Saccharophagus_degradans_2-40 > > I see NCBI has info on it. > http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19331 > > I am not sure where to get hold of gene annotation. > > Thanks for your help! > -Abhi > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ------------------------------ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome End of Genome Digest, Vol 85, Issue 4 ************************************* _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
