Hello, The agp file is in the same place as the hg18 one, just swap out the database name:
http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/bigZips/ Thanks, jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Ariel Paulson" <[email protected]> wrote: > From: "Ariel Paulson" <[email protected]> > To: [email protected] > Sent: Tuesday, August 25, 2009 4:44:39 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] canFam2 AGP > > Tam, > > contigAcc will give you the contig components WRT canFam2, but you > have to get this file: > ftp://ftp.ncbi.nlm.nih.gov/genomes/Canis_familiaris/mapview/allcontig.agp.gz > in order to map these components into refseq accessions. > > Jennifer: Does this file or an equivalent exist for galGal3? I have > the same problem for this build. It seems that UCSC, NCBI, and WUSTL > all use different contig names, so I have no idea what maps to where. > > Thanks > Ariel > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Jennifer > Jackson > Sent: Tuesday, August 25, 2009 6:34 PM > To: Tam Sneddon (NIH/NLM/NCBI) [E] > Cc: [email protected] > Subject: Re: [Genome] canFam2 AGP > > Hello, > There is a file called "contigAcc" included in the database and in > the ftp location. Please examine and see if this file is useful, > Thanks, Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Tam Sneddon (NIH/NLM/NCBI) [E]" <[email protected]> > wrote: > > > From: "Tam Sneddon (NIH/NLM/NCBI) [E]" <[email protected]> > > To: [email protected] > > Sent: Tuesday, August 25, 2009 2:58:11 PM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] canFam2 AGP > > > > Hi: > > > > Thanks for your previous help. > > > > I am now trying to find the equivalent Agp file for Dog Build 2.1 > > (canFam2) as you have for human eg > > > > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromAgp.zip > > > > However, the dog file lists contigs rather than accessions: > > > > > ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam2/bigZips/chromAgp.tar. > > gz > > > > I also find the same information from the Table browser. > > > > How to I find the mapping of the canFam genome to NCBI accessions? > > > > Thanks, > > > > Tam > > > > > > > > -----Original Message----- > > From: Brooke Rhead [mailto:[email protected]] > > Sent: Friday, May 30, 2008 6:51 PM > > To: Sneddon, Tam (NIH/NLM/NCBI) [E] > > Cc: Brooke Rhead > > Subject: Re: [Genome] liftAll.zip > > > > Hi Tam, > > > > In addition to the 'ctgPos' table, there is a 'gold' table that > shows > > > > smaller assembly fragments. Here is a session in mm8 with both of > > these > > > > tracks turned on: > > > > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_oth > > er UserName=Rhead&hgS_otherUserSessionName=mm8.ctgPos.gold > > (You can also get to this by hitting "session" in the blue bar at > the > > > > top of the page and loading the session for user: Rhead and session > > name: mm8.ctgPos.gold .) > > > > However, fragments in 'gold' don't appear to correspond exactly to > the > > > > data from Evan Eichler, either. > > > > -- > > Brooke Rhead > > UCSC Genome Bioinformatics Group > > > > > > Sneddon, Tam (NIH/NLM/NCBI) [E] wrote: > > > Dear Brooke, > > > > > > Thank you for the instructions. > > > > > > However, I have the following data from Evan Eichler for mouse > > build > > 36 > > > that does not appear to have a mapping from the results table I > get > > from > > > UCSC: > > > > > > Strain chr chr_start chr_end > > > C57BL/6J 13_random 148001 163444 > > > C57BL/6J 5_random 330001 366979 > > > C57BL/6J 5_random 416978 612972 > > > C57BL/6J 5_random 1033001 1141437 > > > C57BL/6J 5_random 1191436 1632367 > > > C57BL/6J 5_random 2097001 2118876 > > > C57BL/6J 5_random 2540001 2645529 > > > C57BL/6J Un_random 85799 101594 > > > C57BL/6J Un_random 246001 246876 > > > C57BL/6J Un_random 369001 373030 > > > C57BL/6J Un_random 423029 431442 > > > C57BL/6J Un_random 511001 511472 > > > C57BL/6J Un_random 561471 569583 > > > C57BL/6J Un_random 619582 626111 > > > C57BL/6J Un_random 676110 677715 > > > C57BL/6J Un_random 882001 888125 > > > C57BL/6J Un_random 938124 1111238 > > > C57BL/6J Un_random 1386001 1397961 > > > C57BL/6J Y_random 669001 669190 > > > C57BL/6J Y_random 1408001 1473108 > > > C57BL/6J Y_random 1892001 1897245 > > > C57BL/6J Y_random 6138001 6138132 > > > C57BL/6J Y_random 8291001 8310551 > > > C57BL/6J Y_random 9376001 9378014 > > > C57BL/6J Y_random 9783001 9784330 > > > C57BL/6J Y_random 10153001 10166856 > > > C57BL/6J Y_random 11111001 11131192 > > > C57BL/6J Y_random 11427001 11445003 > > > C57BL/6J Y_random 11778001 11791534 > > > C57BL/6J Y_random 12663001 12669479 > > > C57BL/6J Y_random 13127001 13127544 > > > > > > Do you have mappings to contigs rather than accessions? > > > > > > Thanks, > > > > > > Tam > > > > > > > > > > > > -----Original Message----- > > > From: Brooke Rhead [mailto:[email protected]] > > > Sent: Tuesday, May 27, 2008 7:17 PM > > > To: Sneddon, Tam (NIH/NLM/NCBI) [E] > > > Cc: [email protected] > > > Subject: Re: [Genome] liftAll.zip > > > > > > Hello Tam, > > > > > > We do not have a liftAll.zip file for mm8. However, nearly > > identical > > > information is available in the 'ctgPos' table. To get to it, > make > > the > > > following selections in the Table Browser: > > > > > > clade: vertebrate > > > genome: mouse > > > assembly: Feb. 2006 > > > group: mapping and sequencing tracks > > > track: map contigs > > > table: ctgPos > > > region: genome > > > output format: all fields from selected table > > > > > > The first few rows should look like this: > > > > > > #contig size chrom chromStart chromEnd > > > NT_039169 19418419 chr1 3000000 22418419 > > > NT_039170 52567978 chr1 22420785 74988763 > > > > > > In comparison to the liftAll.zip file, these results are missing > the > > > > > chromosome sizes. The sizes are available in the table > 'chromInfo', > > > > > which you can get from the Table Browser with these settings: > > > > > > clade: vertebrate > > > genome: mouse > > > assembly: Feb. 2006 > > > group: all tables > > > database: mm8 > > > table: chromInfo > > > output format: selected fields from primary and related tables > > > > > > hit "get output" and choose the 'chrom' and 'size' fields. > > > > > > Now you should have all of the information available in the > > liftAll.zip > > > file (but not quite in the same order). You will need to > re-order > > the > > > > > columns and change the contig name format so that includes the > > > chromosome number (NT_039169 will become 1/NT_039169) to get the > > exact > > > > > same format as liftAll.zip. You can use your own tools for this, > > or > > the > > > > > > tools available at Galaxy: http://main.g2.bx.psu.edu/ . > > > > > > -- > > > Brooke Rhead > > > UCSC Genome Bioinformatics Group > > > > > > > > > Sneddon, Tam (NIH/NLM/NCBI) [E] wrote: > > >> Hi: > > >> > > >> Do you have a 'liftAll.zip' file for mm8 in the 'Full data set' > > like > > > you > > >> do for human?: > > >> > > >> http://hgdownload.cse.ucsc.edu/goldenPath/hg17/bigZips/ > > >> > > >> Thanks, > > >> > > >> > > >> > > >> Tam > > >> > > >> ____________________________ > > >> > > >> > > >> > > >> Dr Tam Paterson Sneddon > > >> > > >> Staff Scientist > > >> > > >> DHHS/NIH/NLM/NCBI > > >> > > >> 45 Center Drive - Natcher Building > > >> > > >> Building 45, Room 5AN18D-29 > > >> > > >> Bethesda, MD 20892 > > >> > > >> > > >> > > >> [email protected] > > >> > > >> > > >> > > >> _______________________________________________ > > >> Genome maillist - [email protected] > > >> http://www.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
