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_other 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
