Hi Brandon, UCSC doesn't host any Arabidopsis data, so I can't help with the specifics, but I can point you to some info about chromosome naming schemes, like chrUn, etc. that you had a question about.
Here's some info in our FAQs: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download11 Also, head to the UCSC browser (http://genome.ucsc.edu/cgi-bin/hgGateway) and from the drop-downs, select hg19 (if not already selected). Then scroll down on the page to the section called "Chromosome naming scheme". That should answer your questions regarding "the later regions". - Greg Roe UCSC Genome Browser On 1/22/11 10:33 PM, bldf2b wrote: > Hello, I was wondering if you could help me out or at least point me in the > right direction. > > I'm trying to generate coverage plots for my Solexa data on Arabidopsis, but > in order to do so I need a file containing the chromosomes and their lengths. > > A file similar to this example for humans: > > <Chromosome> /<Chromosome Length> /<file source> > > chr1 249250621 /gbdb/hg19/hg19.2bit > chr2 243199373 /gbdb/hg19/hg19.2bit > chr3 198022430 /gbdb/hg19/hg19.2bit > chr4 191154276 /gbdb/hg19/hg19.2bit > chr5 180915260 /gbdb/hg19/hg19.2bit > chr6 171115067 /gbdb/hg19/hg19.2bit > chr7 159138663 /gbdb/hg19/hg19.2bit > chrX 155270560 /gbdb/hg19/hg19.2bit > chr8 146364022 /gbdb/hg19/hg19.2bit > chr9 141213431 /gbdb/hg19/hg19.2bit > chr10 135534747 /gbdb/hg19/hg19.2bit > chr11 135006516 /gbdb/hg19/hg19.2bit > chr12 133851895 /gbdb/hg19/hg19.2bit > chr13 115169878 /gbdb/hg19/hg19.2bit > chr14 107349540 /gbdb/hg19/hg19.2bit > chr15 102531392 /gbdb/hg19/hg19.2bit > chr16 90354753 /gbdb/hg19/hg19.2bit > chr17 81195210 /gbdb/hg19/hg19.2bit > chr18 78077248 /gbdb/hg19/hg19.2bit > chr20 63025520 /gbdb/hg19/hg19.2bit > chrY 59373566 /gbdb/hg19/hg19.2bit > chr19 59128983 /gbdb/hg19/hg19.2bit > chr22 51304566 /gbdb/hg19/hg19.2bit > chr21 48129895 /gbdb/hg19/hg19.2bit > chr6_ssto_hap7 4928567 /gbdb/hg19/hg19.2bit > chr6_mcf_hap5 4833398 /gbdb/hg19/hg19.2bit > chr6_cox_hap2 4795371 /gbdb/hg19/hg19.2bit > chr6_mann_hap4 4683263 /gbdb/hg19/hg19.2bit > chr6_apd_hap1 4622290 /gbdb/hg19/hg19.2bit > chr6_qbl_hap6 4611984 /gbdb/hg19/hg19.2bit > chr6_dbb_hap3 4610396 /gbdb/hg19/hg19.2bit > chr17_ctg5_hap1 1680828 /gbdb/hg19/hg19.2bit > chr4_ctg9_hap1 590426 /gbdb/hg19/hg19.2bit > chr1_gl000192_random 547496 /gbdb/hg19/hg19.2bit > chrUn_gl000225 211173 /gbdb/hg19/hg19.2bit > chr4_gl000194_random 191469 /gbdb/hg19/hg19.2bit > chr4_gl000193_random 189789 /gbdb/hg19/hg19.2bit > chr9_gl000200_random 187035 /gbdb/hg19/hg19.2bit > chrUn_gl000222 186861 /gbdb/hg19/hg19.2bit > chrUn_gl000212 186858 /gbdb/hg19/hg19.2bit > chr7_gl000195_random 182896 /gbdb/hg19/hg19.2bit > chrUn_gl000223 180455 /gbdb/hg19/hg19.2bit > chrUn_gl000224 179693 /gbdb/hg19/hg19.2bit > chrUn_gl000219 179198 /gbdb/hg19/hg19.2bit > chr17_gl000205_random 174588 /gbdb/hg19/hg19.2bit > chrUn_gl000215 172545 /gbdb/hg19/hg19.2bit > chrUn_gl000216 172294 /gbdb/hg19/hg19.2bit > chrUn_gl000217 172149 /gbdb/hg19/hg19.2bit > chr9_gl000199_random 169874 /gbdb/hg19/hg19.2bit > > > > I would try generating it myself, but I don't understand what the later > regions represent. For example, chrUn_glXXXXXX, in the above case, but they > differ in other organisms. I tried generating a file simply with chr1, chr2, > ch3, ch4, chr5, chrC, and chrM but it did not work. > > @TAIR: I tried locating this or a similar file on your FTP and was > unsuccessful in doing so. > > @UCSC: I found the Arabidopsis mirror site, but it doesn't offer downloads > specifically for Arabidopsis, but I was able to find this file > (chromInfo.txt) for many of the other organisms in your FTP. > > > If either of you could assist me with this issue it would be greatly > appreciated. Generating coverage plots of our data has been in the cards for > a while and upon learning how to generate them, not having this file is > causing a set back. > > Thank you very much for your time. > > > -Brandon > > > Brandon Dinwiddie > University of Missouri - Kansas City > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
